Starting phenix.real_space_refine on Fri Sep 27 22:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/09_2024/7us2_26722.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/09_2024/7us2_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/09_2024/7us2_26722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/09_2024/7us2_26722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/09_2024/7us2_26722.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/09_2024/7us2_26722.cif" } resolution = 2.76 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= -0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 10.66, per 1000 atoms: 0.62 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: 4.49 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.10 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: 5.74 Time building geometry restraints manager: 5.24 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: 10129 17.60 - 35.21: 488 35.21 - 52.81: 112 52.81 - 70.42: 25 70.42 - 88.02: 3 Dihedral angle restraints: 10757 sinusoidal: 4680 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 10754 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: 2.310 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.040 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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= 0.505 Angle : 1.126 23.733 23519 Z= 0.485 Chirality : 0.048 0.297 2558 Planarity : 0.005 0.063 3025 Dihedral : 11.267 88.022 6805 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 (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: -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 TRP 0.011 0.002 TRP B 587 HIS 0.006 0.001 HIS C 552 PHE 0.019 0.002 PHE C 423 TYR 0.010 0.001 TYR E 397 ARG 0.003 0.000 ARG C 620 *********************** 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 fitting. rotamer outliers: 10 poor density : 218 time to evaluate : 2.093 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: D 369 TYR cc_start: 0.7934 (p90) cc_final: 0.7699 (p90) REVERT: E 369 TYR cc_start: 0.7693 (p90) cc_final: 0.7142 (p90) outliers start: 10 outliers final: 2 residues processed: 227 average time/residue: 1.9686 time to fit residues: 481.1401 Evaluate side-chains 98 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 173 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17493 Z= 0.241 Angle : 0.605 9.790 23519 Z= 0.308 Chirality : 0.040 0.203 2558 Planarity : 0.005 0.068 3025 Dihedral : 8.126 86.523 2423 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Rotamer: Outliers : 0.78 % Allowed : 8.39 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.17), residues: 2046 helix: 1.01 (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 TRP 0.008 0.001 TRP E 587 HIS 0.006 0.001 HIS D 552 PHE 0.010 0.001 PHE D 423 TYR 0.015 0.001 TYR F 369 ARG 0.011 0.001 ARG D 518 *********************** 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 111 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 2.114 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: 0.8496 (mp0) cc_final: 0.7684 (mp0) REVERT: D 695 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6578 (ptt90) outliers start: 14 outliers final: 4 residues processed: 105 average time/residue: 1.7012 time to fit residues: 196.5836 Evaluate side-chains 84 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain C residue 486 CYS 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 103 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS B 624 HIS D 624 HIS ** F 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 HIS F 460 HIS ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17493 Z= 0.301 Angle : 0.547 9.938 23519 Z= 0.280 Chirality : 0.040 0.199 2558 Planarity : 0.004 0.048 3025 Dihedral : 7.853 78.507 2419 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 8.11 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.19), residues: 2046 helix: 1.63 (0.15), residues: 1100 sheet: -3.42 (0.25), residues: 257 loop : -0.54 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 587 HIS 0.007 0.001 HIS D 552 PHE 0.010 0.001 PHE D 423 TYR 0.014 0.001 TYR C 322 ARG 0.010 0.001 ARG D 417 *********************** 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 109 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7849 (m-80) cc_final: 0.7438 (m-10) outliers start: 22 outliers final: 7 residues processed: 104 average time/residue: 1.5574 time to fit residues: 180.3280 Evaluate side-chains 81 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 2.271 ------------------------------------------------------------------------------- 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 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP 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 184 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 198 optimal weight: 0.0070 chunk 97 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 418 HIS F 552 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2816 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= 0.189 Angle : 0.506 10.361 23519 Z= 0.258 Chirality : 0.038 0.169 2558 Planarity : 0.003 0.038 3025 Dihedral : 7.733 82.970 2419 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.56 % Favored : 98.39 % Rotamer: Outliers : 0.72 % Allowed : 9.44 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.19), residues: 2046 helix: 1.83 (0.15), residues: 1106 sheet: -3.21 (0.26), residues: 252 loop : -0.48 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 587 HIS 0.006 0.001 HIS F 373 PHE 0.009 0.001 PHE C 423 TYR 0.014 0.001 TYR F 369 ARG 0.010 0.000 ARG D 518 *********************** 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 97 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7868 (m-80) cc_final: 0.7461 (m-10) REVERT: D 695 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6478 (ptt90) REVERT: E 695 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5544 (tpt90) outliers start: 13 outliers final: 2 residues processed: 95 average time/residue: 1.4007 time to fit residues: 149.2580 Evaluate side-chains 77 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain E residue 695 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2998 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= 0.227 Angle : 0.506 11.218 23519 Z= 0.258 Chirality : 0.039 0.159 2558 Planarity : 0.003 0.038 3025 Dihedral : 7.702 89.975 2419 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.94 % Allowed : 9.61 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.19), residues: 2046 helix: 1.97 (0.15), residues: 1106 sheet: -3.09 (0.26), residues: 262 loop : -0.31 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 368 HIS 0.009 0.001 HIS E 373 PHE 0.009 0.001 PHE C 423 TYR 0.023 0.001 TYR F 369 ARG 0.006 0.000 ARG D 417 *********************** 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 95 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7945 (m-80) cc_final: 0.7587 (m-10) REVERT: D 695 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6463 (ptt90) outliers start: 17 outliers final: 7 residues processed: 91 average time/residue: 1.4225 time to fit residues: 145.2913 Evaluate side-chains 80 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 464 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain F residue 412 SER 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 66 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 39 optimal weight: 0.0040 chunk 116 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 chunk 198 optimal weight: 0.0770 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 104 optimal weight: 0.7980 overall best weight: 0.1568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.002 0.041 17493 Z= 0.141 Angle : 0.495 11.925 23519 Z= 0.253 Chirality : 0.038 0.157 2558 Planarity : 0.003 0.037 3025 Dihedral : 7.529 87.364 2419 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.06 % Allowed : 9.78 % 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 (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: 0.90 (0.19), residues: 2046 helix: 2.05 (0.16), residues: 1106 sheet: -2.70 (0.26), residues: 282 loop : -0.27 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.006 0.001 HIS E 373 PHE 0.008 0.001 PHE C 423 TYR 0.028 0.001 TYR F 369 ARG 0.007 0.000 ARG F 554 *********************** 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 109 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7916 (m-80) cc_final: 0.7583 (m-10) REVERT: D 695 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6482 (ptt90) REVERT: E 695 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.5539 (tpt90) outliers start: 19 outliers final: 6 residues processed: 103 average time/residue: 1.4853 time to fit residues: 171.4957 Evaluate side-chains 82 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 486 CYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 197 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17493 Z= 0.191 Angle : 0.518 12.466 23519 Z= 0.262 Chirality : 0.038 0.163 2558 Planarity : 0.003 0.052 3025 Dihedral : 7.573 91.119 2419 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.56 % Allowed : 11.06 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.05 (0.19), residues: 2046 helix: 2.12 (0.16), residues: 1106 sheet: -2.45 (0.26), residues: 272 loop : -0.24 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.007 0.001 HIS E 373 PHE 0.008 0.001 PHE C 423 TYR 0.026 0.001 TYR F 369 ARG 0.011 0.000 ARG D 417 *********************** 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 84 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7966 (m-80) cc_final: 0.7633 (m-10) REVERT: D 695 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6523 (ptt90) REVERT: E 695 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.5599 (tpt90) outliers start: 10 outliers final: 3 residues processed: 81 average time/residue: 1.4390 time to fit residues: 130.8811 Evaluate side-chains 74 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN B 415 GLN B 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3335 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= 0.182 Angle : 0.520 12.710 23519 Z= 0.262 Chirality : 0.038 0.216 2558 Planarity : 0.003 0.039 3025 Dihedral : 7.568 92.313 2419 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.61 % Allowed : 10.83 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.14 (0.19), residues: 2046 helix: 2.14 (0.16), residues: 1106 sheet: -2.32 (0.27), residues: 272 loop : -0.15 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.006 0.001 HIS D 373 PHE 0.007 0.001 PHE E 423 TYR 0.016 0.001 TYR C 322 ARG 0.010 0.000 ARG D 417 *********************** 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 84 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7958 (m-80) cc_final: 0.7696 (m-10) REVERT: D 695 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6495 (ptt90) REVERT: E 695 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.5527 (tpt90) outliers start: 11 outliers final: 5 residues processed: 81 average time/residue: 1.4309 time to fit residues: 130.4824 Evaluate side-chains 76 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL 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 369 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 9.9990 chunk 172 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 144 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 166 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17493 Z= 0.185 Angle : 0.531 12.960 23519 Z= 0.266 Chirality : 0.038 0.224 2558 Planarity : 0.003 0.037 3025 Dihedral : 7.528 92.875 2419 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.33 % Allowed : 11.17 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.16 (0.19), residues: 2046 helix: 2.18 (0.16), residues: 1106 sheet: -2.24 (0.26), residues: 297 loop : -0.10 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.009 0.001 HIS E 373 PHE 0.008 0.001 PHE E 414 TYR 0.016 0.001 TYR C 322 ARG 0.009 0.000 ARG D 417 *********************** 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 77 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7977 (m-80) cc_final: 0.7707 (m-10) REVERT: E 695 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.5563 (tpt90) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 1.4472 time to fit residues: 123.7776 Evaluate side-chains 74 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain E residue 695 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 92 optimal weight: 0.0060 chunk 135 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 17493 Z= 0.163 Angle : 0.528 13.186 23519 Z= 0.264 Chirality : 0.038 0.233 2558 Planarity : 0.003 0.036 3025 Dihedral : 7.414 89.985 2419 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.56 % Allowed : 10.89 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.19 (0.19), residues: 2046 helix: 2.19 (0.16), residues: 1106 sheet: -2.11 (0.26), residues: 297 loop : -0.12 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.010 0.001 HIS D 373 PHE 0.009 0.001 PHE E 414 TYR 0.016 0.001 TYR C 322 ARG 0.011 0.000 ARG D 518 ********************** 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 86 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7964 (m-80) cc_final: 0.7697 (m-10) REVERT: E 695 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.5553 (tpt90) outliers start: 10 outliers final: 6 residues processed: 84 average time/residue: 1.3965 time to fit residues: 132.9993 Evaluate side-chains 74 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 497 VAL 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 695 ARG Chi-restraints excluded: chain F residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 167 optimal weight: 0.0060 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.080502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054811 restraints weight = 57279.821| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.48 r_work: 0.2824 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17493 Z= 0.188 Angle : 0.542 13.040 23519 Z= 0.270 Chirality : 0.039 0.234 2558 Planarity : 0.003 0.035 3025 Dihedral : 7.427 91.819 2419 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.33 % Allowed : 11.17 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.27 (0.19), residues: 2046 helix: 2.22 (0.16), residues: 1106 sheet: -2.00 (0.27), residues: 297 loop : -0.05 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 587 HIS 0.014 0.001 HIS C 373 PHE 0.009 0.001 PHE E 414 TYR 0.015 0.001 TYR C 322 ARG 0.008 0.000 ARG D 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4686.99 seconds wall clock time: 83 minutes 48.76 seconds (5028.76 seconds total)