Starting phenix.real_space_refine on Mon Jul 22 07:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/07_2024/7us2_26722_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/07_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_26722/07_2024/7us2_26722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/07_2024/7us2_26722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/07_2024/7us2_26722_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7us2_26722/07_2024/7us2_26722_neut.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 Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 10.62, 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 - 3.50 Amino acid : False - 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: 6.97 Conformation dependent library (CDL) restraints added in 2.9 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: 2.08 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: 5.53 Time building geometry restraints manager: 7.35 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: 89.16 - 99.13: 25 99.13 - 109.10: 1268 109.10 - 119.07: 13509 119.07 - 129.05: 8528 129.05 - 139.02: 189 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 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: 2.740 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 48.450 Find NCS groups from input model: 1.080 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.560 ------------------------------------------------------------------------------- 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 : 2.226 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: 1.9642 time to fit residues: 480.0569 Evaluate side-chains 98 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 E 455 GLN ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17493 Z= 0.206 Angle : 0.586 8.415 23519 Z= 0.296 Chirality : 0.039 0.202 2558 Planarity : 0.005 0.074 3025 Dihedral : 8.443 85.978 2423 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.42 % Favored : 98.48 % Rotamer: Outliers : 0.78 % Allowed : 8.78 % 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 (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: -0.48 (0.17), residues: 2046 helix: 1.04 (0.15), residues: 1065 sheet: -3.20 (0.26), residues: 207 loop : -1.33 (0.21), residues: 774 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 0.009 0.001 PHE D 423 TYR 0.017 0.001 TYR F 369 ARG 0.010 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 113 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 2.175 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 outliers start: 14 outliers final: 6 residues processed: 108 average time/residue: 1.6164 time to fit residues: 192.3254 Evaluate side-chains 84 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 500 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 HIS D 415 GLN D 624 HIS F 418 HIS F 433 HIS F 460 HIS ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17493 Z= 0.290 Angle : 0.524 9.551 23519 Z= 0.267 Chirality : 0.040 0.154 2558 Planarity : 0.003 0.041 3025 Dihedral : 7.989 102.051 2421 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Rotamer: Outliers : 1.33 % Allowed : 9.17 % Favored : 89.50 % 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: 0.44 (0.19), residues: 2046 helix: 1.70 (0.15), residues: 1100 sheet: -3.32 (0.25), residues: 254 loop : -0.44 (0.23), residues: 692 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 0.015 0.001 TYR C 322 ARG 0.010 0.001 ARG B 327 *********************** 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 107 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7886 (m-80) cc_final: 0.7483 (m-10) REVERT: D 695 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6517 (ptt90) outliers start: 24 outliers final: 8 residues processed: 102 average time/residue: 1.4349 time to fit residues: 163.0450 Evaluate side-chains 87 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain F residue 383 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: 3.9990 chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS F 552 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17493 Z= 0.230 Angle : 0.487 10.685 23519 Z= 0.250 Chirality : 0.038 0.170 2558 Planarity : 0.003 0.038 3025 Dihedral : 7.872 109.553 2421 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.96 % Favored : 98.00 % Rotamer: Outliers : 1.00 % Allowed : 9.94 % Favored : 89.06 % 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: 0.75 (0.19), residues: 2046 helix: 1.90 (0.15), residues: 1111 sheet: -2.80 (0.25), residues: 272 loop : -0.33 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 587 HIS 0.006 0.001 HIS D 552 PHE 0.009 0.001 PHE D 423 TYR 0.014 0.001 TYR C 322 ARG 0.009 0.000 ARG F 555 *********************** 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 99 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7916 (m-80) cc_final: 0.7534 (m-10) REVERT: D 695 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6495 (ptt90) REVERT: E 602 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7996 (m-30) outliers start: 18 outliers final: 7 residues processed: 94 average time/residue: 1.3465 time to fit residues: 142.7571 Evaluate side-chains 86 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 486 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 169 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17493 Z= 0.304 Angle : 0.510 11.035 23519 Z= 0.259 Chirality : 0.040 0.223 2558 Planarity : 0.003 0.039 3025 Dihedral : 7.956 113.053 2421 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 0.83 % Allowed : 10.56 % Favored : 88.61 % 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: 1.00 (0.19), residues: 2046 helix: 2.04 (0.16), residues: 1110 sheet: -2.63 (0.26), residues: 282 loop : -0.05 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 368 HIS 0.007 0.001 HIS E 373 PHE 0.010 0.001 PHE D 423 TYR 0.020 0.001 TYR F 369 ARG 0.006 0.000 ARG D 518 *********************** 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 93 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 2.403 Fit side-chains revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8479 (mp0) cc_final: 0.7094 (mp0) REVERT: A 617 TYR cc_start: 0.7985 (m-80) cc_final: 0.7649 (m-10) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 1.1937 time to fit residues: 120.2671 Evaluate side-chains 77 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 383 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 66 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 39 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 chunk 164 optimal weight: 0.0010 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17493 Z= 0.172 Angle : 0.485 12.086 23519 Z= 0.247 Chirality : 0.038 0.169 2558 Planarity : 0.003 0.039 3025 Dihedral : 7.783 110.103 2421 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.61 % Allowed : 11.06 % Favored : 88.33 % 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: 1.11 (0.19), residues: 2046 helix: 2.07 (0.16), residues: 1111 sheet: -2.40 (0.26), residues: 282 loop : -0.02 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 587 HIS 0.005 0.001 HIS E 373 PHE 0.009 0.001 PHE C 423 TYR 0.027 0.001 TYR F 369 ARG 0.006 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 89 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 2.221 Fit side-chains revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7967 (m-80) cc_final: 0.7645 (m-10) REVERT: D 417 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7817 (ttp80) outliers start: 11 outliers final: 6 residues processed: 87 average time/residue: 1.3805 time to fit residues: 136.0995 Evaluate side-chains 77 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 2.061 ------------------------------------------------------------------------------- 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 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 383 SER 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 191 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17493 Z= 0.194 Angle : 0.493 12.364 23519 Z= 0.250 Chirality : 0.038 0.195 2558 Planarity : 0.003 0.036 3025 Dihedral : 7.697 110.015 2421 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.83 % Allowed : 11.17 % Favored : 88.00 % 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: 1.25 (0.19), residues: 2046 helix: 2.17 (0.16), residues: 1106 sheet: -2.22 (0.27), residues: 282 loop : 0.04 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 587 HIS 0.007 0.001 HIS E 373 PHE 0.008 0.001 PHE C 423 TYR 0.029 0.001 TYR F 369 ARG 0.004 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 91 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 2.082 Fit side-chains revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7995 (m-80) cc_final: 0.7648 (m-10) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 1.3213 time to fit residues: 131.7890 Evaluate side-chains 78 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 486 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 118 optimal weight: 0.0470 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17493 Z= 0.170 Angle : 0.498 12.781 23519 Z= 0.251 Chirality : 0.038 0.203 2558 Planarity : 0.003 0.036 3025 Dihedral : 7.590 108.304 2421 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.50 % Allowed : 11.61 % Favored : 87.89 % 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: 1.37 (0.19), residues: 2046 helix: 2.23 (0.16), residues: 1106 sheet: -2.06 (0.27), residues: 282 loop : 0.12 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 587 HIS 0.008 0.001 HIS E 373 PHE 0.008 0.001 PHE C 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: 9 poor density : 75 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7974 (m-80) cc_final: 0.7702 (m-10) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 1.3652 time to fit residues: 124.9896 Evaluate side-chains 80 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 486 CYS Chi-restraints excluded: chain F residue 500 ASP 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: 0.9990 chunk 184 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8183 moved from start: 0.3366 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= 0.222 Angle : 0.521 13.027 23519 Z= 0.260 Chirality : 0.038 0.223 2558 Planarity : 0.003 0.040 3025 Dihedral : 7.598 109.094 2421 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.56 % Allowed : 11.78 % Favored : 87.67 % 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: 1.40 (0.19), residues: 2046 helix: 2.26 (0.16), residues: 1106 sheet: -2.01 (0.26), residues: 307 loop : 0.21 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 587 HIS 0.010 0.001 HIS E 373 PHE 0.008 0.001 PHE E 414 TYR 0.016 0.001 TYR C 322 ARG 0.010 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 84 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7997 (m-80) cc_final: 0.7719 (m-10) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 1.2864 time to fit residues: 119.8440 Evaluate side-chains 80 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 486 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 0.1980 chunk 204 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17493 Z= 0.175 Angle : 0.519 13.199 23519 Z= 0.259 Chirality : 0.038 0.237 2558 Planarity : 0.003 0.042 3025 Dihedral : 7.503 107.896 2421 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.61 % Allowed : 11.78 % Favored : 87.61 % 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: 1.44 (0.19), residues: 2046 helix: 2.27 (0.16), residues: 1106 sheet: -1.89 (0.26), residues: 307 loop : 0.23 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 587 HIS 0.007 0.001 HIS E 373 PHE 0.008 0.001 PHE E 414 TYR 0.016 0.001 TYR C 322 ARG 0.010 0.000 ARG D 417 ********************** 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: 11 poor density : 75 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: A 617 TYR cc_start: 0.7989 (m-80) cc_final: 0.7714 (m-10) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 1.3412 time to fit residues: 125.8293 Evaluate side-chains 81 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 556 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 486 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 162 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 167 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.080765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056705 restraints weight = 57560.879| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.51 r_work: 0.2789 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17493 Z= 0.167 Angle : 0.506 13.134 23519 Z= 0.253 Chirality : 0.038 0.234 2558 Planarity : 0.003 0.041 3025 Dihedral : 7.423 107.369 2421 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.61 % Allowed : 11.89 % Favored : 87.50 % 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: 1.53 (0.19), residues: 2046 helix: 2.32 (0.16), residues: 1106 sheet: -1.76 (0.27), residues: 307 loop : 0.26 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 587 HIS 0.011 0.001 HIS D 373 PHE 0.008 0.001 PHE E 414 TYR 0.016 0.001 TYR C 322 ARG 0.010 0.000 ARG D 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4588.49 seconds wall clock time: 82 minutes 13.19 seconds (4933.19 seconds total)