Starting phenix.real_space_refine on Sat Jul 4 01:01:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us2_26722/07_2026/7us2_26722.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 60 5.16 5 C 10788 2.51 5 N 3158 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17200 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "C" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "D" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "E" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "F" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2823 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Chain: "P" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.83, per 1000 atoms: 0.22 Number of scatterers: 17200 At special positions: 0 Unit cell: (102.194, 161.634, 152.249, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 18 15.00 Mg 6 11.99 O 3170 8.00 N 3158 7.00 C 10788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 818.3 milliseconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 17 sheets defined 60.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 318 through 337 Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.657A pdb=" N HIS A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 366 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 425 removed outlier: 3.858A pdb=" N PHE A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 445 removed outlier: 3.591A pdb=" N LYS A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 466 through 473 removed outlier: 4.012A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 523 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.521A pdb=" N LEU A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 594 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.557A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 640 removed outlier: 3.736A pdb=" N ILE A 622 " --> pdb=" O GLY A 618 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 337 removed outlier: 3.571A pdb=" N GLN B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.935A pdb=" N HIS B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 366 Processing helix chain 'B' and resid 386 through 399 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 419 through 425 removed outlier: 4.351A pdb=" N PHE B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 466 through 473 removed outlier: 4.036A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 523 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.705A pdb=" N ARG B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 594 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.676A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 630 removed outlier: 3.901A pdb=" N ILE B 622 " --> pdb=" O GLY B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 640 Processing helix chain 'C' and resid 319 through 337 Processing helix chain 'C' and resid 338 through 347 removed outlier: 3.925A pdb=" N HIS C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 366 Processing helix chain 'C' and resid 386 through 400 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.529A pdb=" N ALA C 459 " --> pdb=" O VAL C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 466 through 473 removed outlier: 4.120A pdb=" N LEU C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 523 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 544 through 554 Processing helix chain 'C' and resid 555 through 561 removed outlier: 3.539A pdb=" N LEU C 559 " --> pdb=" O ARG C 555 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.676A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 630 removed outlier: 3.860A pdb=" N ILE C 622 " --> pdb=" O GLY C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 Processing helix chain 'D' and resid 319 through 337 Processing helix chain 'D' and resid 338 through 347 removed outlier: 3.953A pdb=" N HIS D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 366 Processing helix chain 'D' and resid 386 through 400 Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.564A pdb=" N PHE D 406 " --> pdb=" O LYS D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 420 through 425 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 455 through 459 Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 466 through 473 removed outlier: 3.900A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 473 " --> pdb=" O GLN D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 523 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 544 through 554 removed outlier: 3.501A pdb=" N ILE D 548 " --> pdb=" O VAL D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 562 removed outlier: 3.733A pdb=" N ILE D 562 " --> pdb=" O PHE D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 594 Processing helix chain 'D' and resid 602 through 611 removed outlier: 3.657A pdb=" N ALA D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 630 removed outlier: 3.905A pdb=" N ILE D 622 " --> pdb=" O GLY D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 Processing helix chain 'E' and resid 319 through 337 Processing helix chain 'E' and resid 338 through 347 removed outlier: 3.960A pdb=" N HIS E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 366 Processing helix chain 'E' and resid 386 through 400 Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 425 removed outlier: 4.199A pdb=" N PHE E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 446 Processing helix chain 'E' and resid 455 through 459 Processing helix chain 'E' and resid 460 through 465 Processing helix chain 'E' and resid 466 through 473 removed outlier: 3.922A pdb=" N LEU E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU E 473 " --> pdb=" O GLN E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 523 Processing helix chain 'E' and resid 537 through 544 Processing helix chain 'E' and resid 544 through 554 removed outlier: 3.639A pdb=" N ILE E 548 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 561 Processing helix chain 'E' and resid 572 through 594 Processing helix chain 'E' and resid 602 through 610 removed outlier: 3.588A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 613 No H-bonds generated for 'chain 'E' and resid 611 through 613' Processing helix chain 'E' and resid 618 through 630 removed outlier: 3.951A pdb=" N ILE E 622 " --> pdb=" O GLY E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 640 Processing helix chain 'F' and resid 319 through 337 Processing helix chain 'F' and resid 338 through 347 removed outlier: 3.607A pdb=" N ARG F 342 " --> pdb=" O PRO F 338 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS F 346 " --> pdb=" O ARG F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 366 Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.526A pdb=" N GLU F 419 " --> pdb=" O GLU F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.726A pdb=" N ILE F 424 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 446 Processing helix chain 'F' and resid 455 through 459 Processing helix chain 'F' and resid 460 through 474 Processing helix chain 'F' and resid 498 through 523 Processing helix chain 'F' and resid 537 through 544 Processing helix chain 'F' and resid 544 through 554 Processing helix chain 'F' and resid 555 through 561 Processing helix chain 'F' and resid 572 through 594 Processing helix chain 'F' and resid 602 through 611 removed outlier: 3.654A pdb=" N ALA F 606 " --> pdb=" O ASP F 602 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 630 removed outlier: 3.981A pdb=" N ILE F 622 " --> pdb=" O GLY F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 640 Processing sheet with id=AA1, first strand: chain 'A' and resid 375 through 376 removed outlier: 6.344A pdb=" N LEU A 375 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N MET A 493 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 407 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP A 454 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 409 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 375 through 376 removed outlier: 6.344A pdb=" N LEU A 375 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N MET A 493 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 381 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 380 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 653 removed outlier: 3.505A pdb=" N THR A 648 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 683 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 690 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 375 through 376 removed outlier: 6.479A pdb=" N LEU B 375 " --> pdb=" O PHE B 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 494 through 495 removed outlier: 6.022A pdb=" N PHE B 379 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 380 " --> pdb=" O PHE B 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.630A pdb=" N ILE B 407 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP B 454 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 409 " --> pdb=" O ASP B 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 597 through 601 removed outlier: 6.056A pdb=" N THR B 598 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 651 " --> pdb=" O THR B 598 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 600 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N VAL B 653 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 648 " --> pdb=" O ILE B 683 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 406 through 410 removed outlier: 6.518A pdb=" N LEU C 375 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N MET C 493 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE C 377 " --> pdb=" O MET C 493 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER C 495 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C 379 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 475 through 477 removed outlier: 3.731A pdb=" N LEU C 476 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 484 " --> pdb=" O LEU C 476 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 598 through 601 removed outlier: 6.309A pdb=" N THR C 598 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE C 651 " --> pdb=" O THR C 598 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 600 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N VAL C 653 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 648 " --> pdb=" O ILE C 683 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 408 through 410 removed outlier: 3.619A pdb=" N GLY D 381 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL D 376 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL D 566 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU D 378 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE D 568 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU D 380 " --> pdb=" O PHE D 568 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 597 through 600 removed outlier: 6.397A pdb=" N THR D 598 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE D 651 " --> pdb=" O THR D 598 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU D 600 " --> pdb=" O ILE D 651 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N VAL D 653 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D 648 " --> pdb=" O ILE D 683 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 406 through 410 removed outlier: 6.922A pdb=" N LEU E 375 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N MET E 493 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE E 377 " --> pdb=" O MET E 493 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N SER E 495 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE E 379 " --> pdb=" O SER E 495 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL E 376 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL E 566 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU E 378 " --> pdb=" O VAL E 566 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE E 568 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU E 380 " --> pdb=" O PHE E 568 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 598 through 600 removed outlier: 5.790A pdb=" N THR E 598 " --> pdb=" O LEU E 649 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE E 651 " --> pdb=" O THR E 598 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU E 600 " --> pdb=" O ILE E 651 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL E 653 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 648 " --> pdb=" O ILE E 683 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 408 through 410 removed outlier: 6.883A pdb=" N LEU F 409 " --> pdb=" O ASP F 454 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY F 381 " --> pdb=" O SER F 495 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL F 376 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL F 566 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU F 378 " --> pdb=" O VAL F 566 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE F 568 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU F 380 " --> pdb=" O PHE F 568 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 475 through 477 Processing sheet with id=AB8, first strand: chain 'F' and resid 600 through 601 removed outlier: 6.895A pdb=" N LEU F 600 " --> pdb=" O ILE F 651 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N VAL F 653 " --> pdb=" O LEU F 600 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR F 648 " --> pdb=" O ILE F 683 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 683 " --> pdb=" O THR F 648 " (cutoff:3.500A) 871 hydrogen bonds defined for protein. 2565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 5904 1.36 - 1.49: 4088 1.49 - 1.63: 7399 1.63 - 1.76: 3 1.76 - 1.89: 99 Bond restraints: 17493 Sorted by residual: bond pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sigma weight residual 1.585 1.871 -0.286 2.70e-02 1.37e+03 1.12e+02 bond pdb=" O3B AGS C 801 " pdb=" PB AGS C 801 " ideal model delta sigma weight residual 1.585 1.859 -0.274 2.70e-02 1.37e+03 1.03e+02 bond pdb=" O3B AGS F 801 " pdb=" PB AGS F 801 " ideal model delta sigma weight residual 1.585 1.856 -0.271 2.70e-02 1.37e+03 1.01e+02 bond pdb=" O3B AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sigma weight residual 1.585 1.856 -0.271 2.70e-02 1.37e+03 1.01e+02 bond pdb=" O3B AGS E 801 " pdb=" PB AGS E 801 " ideal model delta sigma weight residual 1.585 1.854 -0.269 2.70e-02 1.37e+03 9.90e+01 ... (remaining 17488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 23367 4.75 - 9.49: 92 9.49 - 14.24: 17 14.24 - 18.99: 37 18.99 - 23.73: 6 Bond angle restraints: 23519 Sorted by residual: angle pdb=" PB AGS D 801 " pdb=" O3B AGS D 801 " pdb=" PG AGS D 801 " ideal model delta sigma weight residual 120.12 139.02 -18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" PB AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sigma weight residual 120.12 138.95 -18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" PB AGS E 801 " pdb=" O3B AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 120.12 138.47 -18.35 3.00e+00 1.11e-01 3.74e+01 angle pdb=" O1B AGS F 801 " pdb=" PB AGS F 801 " pdb=" O3B AGS F 801 " ideal model delta sigma weight residual 109.95 91.68 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" O1B AGS B 801 " pdb=" PB AGS B 801 " pdb=" O3B AGS B 801 " ideal model delta sigma weight residual 109.95 91.72 18.23 3.00e+00 1.11e-01 3.69e+01 ... (remaining 23514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 10123 17.60 - 35.21: 463 35.21 - 52.81: 91 52.81 - 70.42: 11 70.42 - 88.02: 3 Dihedral angle restraints: 10691 sinusoidal: 4614 harmonic: 6077 Sorted by residual: dihedral pdb=" CA VAL E 630 " pdb=" C VAL E 630 " pdb=" N VAL E 631 " pdb=" CA VAL E 631 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA VAL F 630 " pdb=" C VAL F 630 " pdb=" N VAL F 631 " pdb=" CA VAL F 631 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA VAL D 630 " pdb=" C VAL D 630 " pdb=" N VAL D 631 " pdb=" CA VAL D 631 " ideal model delta harmonic sigma weight residual -180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 10688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2191 0.059 - 0.119: 283 0.119 - 0.178: 72 0.178 - 0.238: 5 0.238 - 0.297: 7 Chirality restraints: 2558 Sorted by residual: chirality pdb=" C2' AGS A 801 " pdb=" C1' AGS A 801 " pdb=" C3' AGS A 801 " pdb=" O2' AGS A 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.97 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' AGS F 801 " pdb=" C1' AGS F 801 " pdb=" C3' AGS F 801 " pdb=" O2' AGS F 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.96 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' AGS E 801 " pdb=" C1' AGS E 801 " pdb=" C3' AGS E 801 " pdb=" O2' AGS E 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.95 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2555 not shown) Planarity restraints: 3025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 546 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO F 547 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 547 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 547 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 546 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO B 547 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 546 " -0.034 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO E 547 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 547 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 547 " -0.029 5.00e-02 4.00e+02 ... (remaining 3022 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 112 2.56 - 3.14: 13298 3.14 - 3.73: 27027 3.73 - 4.31: 38420 4.31 - 4.90: 64105 Nonbonded interactions: 142962 Sorted by model distance: nonbonded pdb=" OG1 THR D 388 " pdb="MG MG D 802 " model vdw 1.974 2.170 nonbonded pdb=" OG1 THR C 388 " pdb="MG MG C 802 " model vdw 1.974 2.170 nonbonded pdb=" OG1 THR E 388 " pdb="MG MG E 802 " model vdw 1.975 2.170 nonbonded pdb=" OG1 THR B 388 " pdb="MG MG B 802 " model vdw 1.984 2.170 nonbonded pdb=" O1B AGS A 801 " pdb="MG MG A 802 " model vdw 1.996 2.170 ... (remaining 142957 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.480 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.009 0.286 17493 Z= 0.397 Angle : 1.126 23.733 23519 Z= 0.485 Chirality : 0.048 0.297 2558 Planarity : 0.005 0.063 3025 Dihedral : 10.605 88.022 6739 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.06 % Rotamer: Outliers : 0.56 % Allowed : 3.22 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.15), residues: 2046 helix: -1.02 (0.12), residues: 1064 sheet: -3.97 (0.23), residues: 192 loop : -2.06 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 620 TYR 0.010 0.001 TYR E 397 PHE 0.019 0.002 PHE C 423 TRP 0.011 0.002 TRP B 587 HIS 0.006 0.001 HIS C 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.40 (17493) covalent geometry : angle 1.12618 / 0.49 (23519) hydrogen bonds : bond 0.15099 / 10.40 ( 871) hydrogen bonds : angle 7.31095 / 5.22 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.708 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: D 369 TYR cc_start: 0.7934 (p90) cc_final: 0.7699 (p90) REVERT: E 369 TYR cc_start: 0.7693 (p90) cc_final: 0.7141 (p90) outliers start: 10 outliers final: 2 residues processed: 227 average time/residue: 0.9595 time to fit residues: 233.6922 Evaluate side-chains 99 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain E residue 602 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 563 ASN E 415 GLN ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.081456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056072 restraints weight = 56784.292| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.46 r_work: 0.2843 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17493 Z= 0.162 Angle : 0.607 9.498 23519 Z= 0.309 Chirality : 0.040 0.210 2558 Planarity : 0.005 0.061 3025 Dihedral : 7.097 91.249 2357 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Rotamer: Outliers : 0.72 % Allowed : 8.50 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2046 helix: 0.96 (0.14), residues: 1069 sheet: -3.31 (0.26), residues: 207 loop : -1.33 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 518 TYR 0.018 0.001 TYR F 369 PHE 0.010 0.001 PHE D 423 TRP 0.008 0.001 TRP E 587 HIS 0.006 0.001 HIS D 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (17493) covalent geometry : angle 0.60717 / 0.31 (23519) hydrogen bonds : bond 0.04163 / 2.84 ( 871) hydrogen bonds : angle 5.47524 / 3.97 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.9125 (mp0) cc_final: 0.8410 (mp0) REVERT: B 372 GLU cc_start: 0.8780 (mp0) cc_final: 0.8489 (mp0) REVERT: B 487 LYS cc_start: 0.9324 (mttt) cc_final: 0.9119 (mtpp) REVERT: C 327 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8789 (ptm-80) REVERT: C 695 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6997 (ttt90) REVERT: D 695 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6949 (ptt90) REVERT: E 467 MET cc_start: 0.9230 (mtt) cc_final: 0.9022 (mtt) REVERT: F 467 MET cc_start: 0.9329 (mtp) cc_final: 0.8937 (mtm) REVERT: F 473 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9024 (mp0) outliers start: 13 outliers final: 4 residues processed: 105 average time/residue: 0.7600 time to fit residues: 86.8757 Evaluate side-chains 87 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 695 ARG Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain F residue 486 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 192 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 164 optimal weight: 0.1980 chunk 137 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 433 HIS F 460 HIS F 552 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.081297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.055665 restraints weight = 57769.562| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.53 r_work: 0.2823 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17493 Z= 0.128 Angle : 0.524 10.170 23519 Z= 0.267 Chirality : 0.039 0.206 2558 Planarity : 0.004 0.051 3025 Dihedral : 6.689 76.720 2353 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.91 % Favored : 98.00 % Rotamer: Outliers : 1.33 % Allowed : 8.22 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 2046 helix: 1.71 (0.15), residues: 1070 sheet: -3.45 (0.25), residues: 257 loop : -0.66 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 417 TYR 0.014 0.001 TYR C 322 PHE 0.008 0.001 PHE C 423 TRP 0.007 0.001 TRP D 587 HIS 0.006 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (17493) covalent geometry : angle 0.52400 / 0.27 (23519) hydrogen bonds : bond 0.03499 / 2.39 ( 871) hydrogen bonds : angle 5.03482 / 3.68 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8952 (mp0) cc_final: 0.8690 (mp0) REVERT: A 501 GLU cc_start: 0.9038 (mp0) cc_final: 0.8775 (mp0) REVERT: B 372 GLU cc_start: 0.8860 (mp0) cc_final: 0.8553 (mp0) REVERT: C 327 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8834 (ptm-80) REVERT: C 403 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8928 (mmmt) REVERT: C 695 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7046 (ttt90) REVERT: E 695 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6830 (tpt90) REVERT: F 473 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8923 (mp0) REVERT: F 552 HIS cc_start: 0.8674 (t70) cc_final: 0.8450 (t-90) outliers start: 24 outliers final: 6 residues processed: 113 average time/residue: 0.7756 time to fit residues: 95.9948 Evaluate side-chains 90 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 695 ARG Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 486 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 19 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 469 GLN B 505 HIS B 624 HIS C 505 HIS D 624 HIS E 415 GLN F 418 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.079662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053826 restraints weight = 58368.299| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.50 r_work: 0.2771 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17493 Z= 0.213 Angle : 0.531 10.238 23519 Z= 0.271 Chirality : 0.040 0.167 2558 Planarity : 0.003 0.042 3025 Dihedral : 6.382 74.855 2353 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Rotamer: Outliers : 0.89 % Allowed : 9.00 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 2046 helix: 1.78 (0.15), residues: 1111 sheet: -3.14 (0.26), residues: 257 loop : -0.38 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 327 TYR 0.016 0.001 TYR F 369 PHE 0.011 0.001 PHE D 423 TRP 0.008 0.001 TRP F 368 HIS 0.007 0.001 HIS D 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (17493) covalent geometry : angle 0.53070 / 0.27 (23519) hydrogen bonds : bond 0.03535 / 2.41 ( 871) hydrogen bonds : angle 4.90813 / 3.57 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9012 (mp0) cc_final: 0.8748 (mp0) REVERT: A 501 GLU cc_start: 0.9109 (mp0) cc_final: 0.8739 (mp0) REVERT: A 617 TYR cc_start: 0.9194 (m-80) cc_final: 0.8857 (m-10) REVERT: B 372 GLU cc_start: 0.8860 (mp0) cc_final: 0.8530 (mp0) REVERT: B 542 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: C 695 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7131 (ttt90) REVERT: D 695 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6925 (ptt90) REVERT: E 695 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6800 (tpt90) REVERT: F 473 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8998 (mp0) outliers start: 16 outliers final: 3 residues processed: 99 average time/residue: 0.7094 time to fit residues: 77.3247 Evaluate side-chains 80 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 695 ARG Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 412 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 100 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.080136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054310 restraints weight = 58088.527| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.56 r_work: 0.2787 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17493 Z= 0.141 Angle : 0.496 11.301 23519 Z= 0.255 Chirality : 0.039 0.160 2558 Planarity : 0.003 0.038 3025 Dihedral : 6.220 69.886 2353 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.06 % Allowed : 9.67 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 2046 helix: 1.88 (0.15), residues: 1111 sheet: -2.94 (0.25), residues: 284 loop : -0.25 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 555 TYR 0.024 0.001 TYR F 369 PHE 0.009 0.001 PHE F 553 TRP 0.007 0.001 TRP F 368 HIS 0.008 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17493) covalent geometry : angle 0.49623 / 0.25 (23519) hydrogen bonds : bond 0.03260 / 2.22 ( 871) hydrogen bonds : angle 4.78068 / 3.48 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9026 (mp0) cc_final: 0.8724 (mp0) REVERT: A 411 MET cc_start: 0.8492 (tpp) cc_final: 0.8248 (mmm) REVERT: A 501 GLU cc_start: 0.9063 (mp0) cc_final: 0.8614 (mp0) REVERT: A 617 TYR cc_start: 0.9180 (m-80) cc_final: 0.8900 (m-10) REVERT: B 372 GLU cc_start: 0.8856 (mp0) cc_final: 0.8532 (mp0) REVERT: B 542 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: C 403 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8778 (mmmt) REVERT: C 695 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7260 (ttt180) REVERT: D 695 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6882 (ptt90) REVERT: E 695 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6837 (tpt90) REVERT: F 473 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8909 (mp0) outliers start: 19 outliers final: 7 residues processed: 97 average time/residue: 0.6627 time to fit residues: 71.7159 Evaluate side-chains 86 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 695 ARG Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 556 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 41 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.080214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054595 restraints weight = 57528.543| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.52 r_work: 0.2793 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17493 Z= 0.125 Angle : 0.490 11.902 23519 Z= 0.251 Chirality : 0.038 0.162 2558 Planarity : 0.003 0.037 3025 Dihedral : 6.124 65.288 2353 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.22 % Allowed : 9.61 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 2046 helix: 1.98 (0.16), residues: 1111 sheet: -2.75 (0.26), residues: 282 loop : -0.17 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 620 TYR 0.025 0.001 TYR F 369 PHE 0.009 0.001 PHE C 423 TRP 0.006 0.001 TRP D 587 HIS 0.004 0.001 HIS D 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (17493) covalent geometry : angle 0.49048 / 0.25 (23519) hydrogen bonds : bond 0.03132 / 2.13 ( 871) hydrogen bonds : angle 4.66739 / 3.40 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9055 (mp0) cc_final: 0.8748 (mp0) REVERT: A 501 GLU cc_start: 0.9070 (mp0) cc_final: 0.8664 (mp0) REVERT: A 617 TYR cc_start: 0.9195 (m-80) cc_final: 0.8914 (m-10) REVERT: B 372 GLU cc_start: 0.8866 (mp0) cc_final: 0.8532 (mp0) REVERT: B 467 MET cc_start: 0.9270 (mtt) cc_final: 0.8934 (mtm) REVERT: B 542 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8614 (mp0) REVERT: C 403 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8789 (mmmt) REVERT: D 488 ASP cc_start: 0.9286 (m-30) cc_final: 0.8938 (p0) REVERT: D 695 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6879 (ptt90) REVERT: E 695 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6864 (tpt90) REVERT: F 473 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8876 (mp0) outliers start: 22 outliers final: 8 residues processed: 100 average time/residue: 0.6433 time to fit residues: 71.4431 Evaluate side-chains 87 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 556 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 GLN B 415 GLN B 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.080039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054387 restraints weight = 57860.805| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.50 r_work: 0.2789 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17493 Z= 0.135 Angle : 0.502 12.394 23519 Z= 0.255 Chirality : 0.039 0.189 2558 Planarity : 0.003 0.046 3025 Dihedral : 6.079 63.464 2353 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.78 % Allowed : 10.11 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 2046 helix: 2.03 (0.16), residues: 1111 sheet: -2.50 (0.27), residues: 272 loop : -0.14 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 417 TYR 0.019 0.001 TYR F 369 PHE 0.008 0.001 PHE C 423 TRP 0.006 0.001 TRP D 587 HIS 0.006 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (17493) covalent geometry : angle 0.50198 / 0.25 (23519) hydrogen bonds : bond 0.03081 / 2.11 ( 871) hydrogen bonds : angle 4.61471 / 3.36 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9075 (mp0) cc_final: 0.8743 (mp0) REVERT: A 501 GLU cc_start: 0.9076 (mp0) cc_final: 0.8676 (mp0) REVERT: A 617 TYR cc_start: 0.9186 (m-80) cc_final: 0.8930 (m-10) REVERT: B 372 GLU cc_start: 0.8882 (mp0) cc_final: 0.8529 (mp0) REVERT: B 467 MET cc_start: 0.9279 (mtt) cc_final: 0.8933 (mtm) REVERT: B 542 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: D 488 ASP cc_start: 0.9270 (m-30) cc_final: 0.8969 (p0) REVERT: D 518 ARG cc_start: 0.9032 (ptp-110) cc_final: 0.8807 (mtm110) REVERT: D 695 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6859 (ptt90) REVERT: E 695 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6904 (tpt90) REVERT: F 473 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8880 (mp0) outliers start: 14 outliers final: 7 residues processed: 90 average time/residue: 0.7005 time to fit residues: 69.8261 Evaluate side-chains 83 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 556 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 183 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.080058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054282 restraints weight = 57898.187| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.55 r_work: 0.2786 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17493 Z= 0.130 Angle : 0.519 12.754 23519 Z= 0.261 Chirality : 0.038 0.200 2558 Planarity : 0.003 0.052 3025 Dihedral : 6.044 60.084 2353 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.61 % Allowed : 10.56 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2046 helix: 2.07 (0.16), residues: 1111 sheet: -2.42 (0.26), residues: 297 loop : -0.08 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 417 TYR 0.016 0.001 TYR C 322 PHE 0.008 0.001 PHE C 423 TRP 0.006 0.001 TRP D 587 HIS 0.008 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17493) covalent geometry : angle 0.51940 / 0.26 (23519) hydrogen bonds : bond 0.03021 / 2.06 ( 871) hydrogen bonds : angle 4.57303 / 3.32 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9084 (mp0) cc_final: 0.8757 (mp0) REVERT: A 501 GLU cc_start: 0.9073 (mp0) cc_final: 0.8683 (mp0) REVERT: A 617 TYR cc_start: 0.9179 (m-80) cc_final: 0.8937 (m-10) REVERT: B 372 GLU cc_start: 0.8879 (mp0) cc_final: 0.8521 (mp0) REVERT: B 467 MET cc_start: 0.9294 (mtt) cc_final: 0.8994 (mtm) REVERT: B 542 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8621 (mp0) REVERT: D 488 ASP cc_start: 0.9264 (m-30) cc_final: 0.8966 (p0) REVERT: D 695 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6826 (ptt90) REVERT: E 695 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6829 (tpt90) REVERT: F 473 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8853 (mp0) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.6933 time to fit residues: 67.8519 Evaluate side-chains 86 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain E residue 467 MET Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 556 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 32 optimal weight: 6.9990 chunk 152 optimal weight: 0.0020 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.080291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054531 restraints weight = 58129.220| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.52 r_work: 0.2794 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17493 Z= 0.118 Angle : 0.521 14.095 23519 Z= 0.260 Chirality : 0.038 0.219 2558 Planarity : 0.003 0.053 3025 Dihedral : 6.005 55.737 2353 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.78 % Allowed : 10.56 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 2046 helix: 2.10 (0.16), residues: 1111 sheet: -2.27 (0.26), residues: 297 loop : 0.00 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 518 TYR 0.016 0.001 TYR C 322 PHE 0.013 0.001 PHE E 414 TRP 0.006 0.001 TRP D 587 HIS 0.009 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17493) covalent geometry : angle 0.52135 / 0.26 (23519) hydrogen bonds : bond 0.02951 / 2.02 ( 871) hydrogen bonds : angle 4.52088 / 3.29 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9088 (mp0) cc_final: 0.8755 (mp0) REVERT: A 501 GLU cc_start: 0.9051 (mp0) cc_final: 0.8667 (mp0) REVERT: A 617 TYR cc_start: 0.9180 (m-80) cc_final: 0.8970 (m-10) REVERT: B 372 GLU cc_start: 0.8880 (mp0) cc_final: 0.8493 (mp0) REVERT: B 467 MET cc_start: 0.9277 (mtt) cc_final: 0.8954 (mtm) REVERT: B 542 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8620 (mp0) REVERT: C 403 LYS cc_start: 0.9382 (mtmm) cc_final: 0.9149 (mmmt) REVERT: D 488 ASP cc_start: 0.9261 (m-30) cc_final: 0.8943 (p0) REVERT: E 695 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6831 (tpt90) REVERT: F 473 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8842 (mp0) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 0.6350 time to fit residues: 60.8925 Evaluate side-chains 83 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain E residue 467 MET Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 556 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 125 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.079879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054113 restraints weight = 57707.790| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.49 r_work: 0.2782 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17493 Z= 0.142 Angle : 0.536 13.329 23519 Z= 0.266 Chirality : 0.039 0.223 2558 Planarity : 0.003 0.058 3025 Dihedral : 5.996 54.623 2353 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.56 % Allowed : 10.78 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2046 helix: 2.12 (0.16), residues: 1111 sheet: -2.15 (0.26), residues: 297 loop : 0.04 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 518 TYR 0.016 0.001 TYR C 322 PHE 0.010 0.001 PHE E 414 TRP 0.005 0.001 TRP D 587 HIS 0.010 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (17493) covalent geometry : angle 0.53622 / 0.27 (23519) hydrogen bonds : bond 0.03009 / 2.06 ( 871) hydrogen bonds : angle 4.52956 / 3.29 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9093 (mp0) cc_final: 0.8761 (mp0) REVERT: A 467 MET cc_start: 0.8949 (mpp) cc_final: 0.8681 (mtm) REVERT: A 501 GLU cc_start: 0.9043 (mp0) cc_final: 0.8676 (mp0) REVERT: A 617 TYR cc_start: 0.9214 (m-80) cc_final: 0.8994 (m-10) REVERT: B 372 GLU cc_start: 0.8877 (mp0) cc_final: 0.8500 (mp0) REVERT: B 467 MET cc_start: 0.9274 (mtt) cc_final: 0.8979 (mtm) REVERT: B 542 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8619 (mp0) REVERT: C 403 LYS cc_start: 0.9374 (mtmm) cc_final: 0.9136 (mmmt) REVERT: D 488 ASP cc_start: 0.9262 (m-30) cc_final: 0.8951 (p0) REVERT: E 695 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6838 (tpt90) REVERT: F 473 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8888 (mp0) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.6826 time to fit residues: 62.3743 Evaluate side-chains 80 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain E residue 467 MET Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain F residue 556 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.080031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.054399 restraints weight = 58091.018| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.53 r_work: 0.2793 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17493 Z= 0.125 Angle : 0.527 13.175 23519 Z= 0.262 Chirality : 0.038 0.227 2558 Planarity : 0.003 0.057 3025 Dihedral : 5.986 53.697 2353 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.56 % Allowed : 10.72 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2046 helix: 2.13 (0.16), residues: 1111 sheet: -2.05 (0.27), residues: 297 loop : 0.08 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 518 TYR 0.016 0.001 TYR C 322 PHE 0.009 0.001 PHE E 414 TRP 0.006 0.001 TRP D 587 HIS 0.011 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17493) covalent geometry : angle 0.52684 / 0.26 (23519) hydrogen bonds : bond 0.02941 / 2.01 ( 871) hydrogen bonds : angle 4.48548 / 3.26 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5695.39 seconds wall clock time: 97 minutes 59.67 seconds (5879.67 seconds total)