Starting phenix.real_space_refine on Fri Jul 3 20:26:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.map" model { file = "/net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ttr_26121/07_2026/7ttr_26121.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.070 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 14 5.49 5 Mg 4 5.21 5 S 54 5.16 5 C 9890 2.51 5 N 2841 2.21 5 O 2894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15697 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2464 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain breaks: 1 Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2517 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Chain: "C" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2643 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2683 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2464 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 294} Chain breaks: 1 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} Time building chain proxies: 3.73, per 1000 atoms: 0.24 Number of scatterers: 15697 At special positions: 0 Unit cell: (109.385, 146.125, 131.93, 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 54 16.00 P 14 15.00 Mg 4 11.99 O 2894 8.00 N 2841 7.00 C 9890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 667.9 milliseconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 15 sheets defined 59.3% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.739A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (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 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' 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 Processing helix chain 'A' and resid 437 through 444 Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 460 through 474 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.683A pdb=" N HIS A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.664A pdb=" N GLY A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 590 Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 614 through 617 Processing helix chain 'A' and resid 618 through 641 removed outlier: 3.569A pdb=" N ARG A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.563A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.898A 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 415 removed outlier: 3.823A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 415' 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: 4.281A pdb=" N PHE B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 424 " --> pdb=" O VAL B 420 " (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 466 removed outlier: 3.680A pdb=" N LEU B 464 " --> pdb=" O HIS B 460 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 466' Processing helix chain 'B' and resid 466 through 474 removed outlier: 4.382A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 removed outlier: 3.709A pdb=" N GLN B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.673A pdb=" N LEU B 559 " --> pdb=" O ARG B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.784A pdb=" N GLY B 612 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 630 Processing helix chain 'B' and resid 630 through 640 Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.528A pdb=" N GLU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 366 Processing helix chain 'C' and resid 386 through 399 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 removed outlier: 3.870A pdb=" N ILE C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.617A pdb=" N LEU C 464 " --> pdb=" O HIS C 460 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 465' Processing helix chain 'C' and resid 466 through 474 removed outlier: 4.196A pdb=" N LEU C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 507 through 512 removed outlier: 4.204A pdb=" N GLU C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 553 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 572 through 596 Processing helix chain 'C' and resid 602 through 611 removed outlier: 4.196A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 630 removed outlier: 3.772A pdb=" N ILE C 622 " --> pdb=" O GLY C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 338 through 347 removed outlier: 3.642A 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 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' 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 removed outlier: 3.916A pdb=" N ILE D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 446 Processing helix chain 'D' and resid 456 through 459 Processing helix chain 'D' and resid 460 through 474 removed outlier: 4.003A pdb=" N ILE D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 514 Processing helix chain 'D' and resid 539 through 544 Processing helix chain 'D' and resid 544 through 554 removed outlier: 3.547A pdb=" N ILE D 548 " --> pdb=" O VAL D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 561 removed outlier: 3.554A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 602 through 611 Processing helix chain 'D' and resid 612 through 613 No H-bonds generated for 'chain 'D' and resid 612 through 613' Processing helix chain 'D' and resid 614 through 617 Processing helix chain 'D' and resid 618 through 630 removed outlier: 3.832A pdb=" N ILE D 622 " --> pdb=" O GLY D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 638 Processing helix chain 'E' and resid 328 through 335 removed outlier: 3.575A pdb=" N ARG E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 3.543A pdb=" N GLU E 345 " --> pdb=" O GLN E 341 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 367 Processing helix chain 'E' and resid 386 through 400 Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 416 through 419 Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.780A pdb=" N ILE E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 446 removed outlier: 3.575A pdb=" N LYS E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 Processing helix chain 'E' and resid 460 through 474 Processing helix chain 'E' and resid 498 through 517 Processing helix chain 'E' and resid 538 through 554 Proline residue: E 547 - end of helix Processing helix chain 'E' and resid 555 through 562 Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 602 through 611 Processing helix chain 'E' and resid 618 through 630 removed outlier: 3.785A pdb=" N ILE E 622 " --> pdb=" O GLY E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 639 removed outlier: 4.187A pdb=" N GLU E 639 " --> pdb=" O ALA E 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 337 removed outlier: 3.913A pdb=" N PHE F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 removed outlier: 4.034A 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 410 through 414 Processing helix chain 'F' and resid 418 through 423 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 455 through 459 Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 468 through 471 Processing helix chain 'F' and resid 498 through 504 removed outlier: 4.219A pdb=" N ILE F 502 " --> pdb=" O ALA F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 548 through 554 Processing helix chain 'F' and resid 572 through 591 Processing helix chain 'F' and resid 593 through 597 Processing helix chain 'F' and resid 601 through 611 removed outlier: 3.635A pdb=" N ASP F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 630 removed outlier: 4.132A 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 406 through 410 removed outlier: 6.704A pdb=" N ILE A 407 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP A 454 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 409 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 451 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR A 494 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 453 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 376 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 566 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 378 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 477 Processing sheet with id=AA3, first strand: chain 'B' and resid 406 through 410 removed outlier: 6.806A pdb=" N VAL B 376 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B 566 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 378 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE B 568 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 380 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 477 Processing sheet with id=AA5, first strand: chain 'B' and resid 598 through 601 removed outlier: 6.595A pdb=" N THR B 598 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 651 " --> pdb=" O THR B 598 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 600 " --> pdb=" O ILE B 651 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 406 through 410 removed outlier: 6.239A pdb=" N VAL C 451 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR C 494 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 453 " --> pdb=" O THR C 494 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 381 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 475 through 477 Processing sheet with id=AA8, first strand: chain 'C' and resid 598 through 601 removed outlier: 6.062A pdb=" N THR C 598 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE C 651 " --> pdb=" O THR C 598 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU C 600 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL C 653 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 406 through 410 removed outlier: 6.698A pdb=" N VAL D 376 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL D 566 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 378 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE D 568 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 380 " --> pdb=" O PHE D 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 598 through 600 removed outlier: 5.767A pdb=" N THR D 598 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU D 649 " --> pdb=" O THR D 598 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 600 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE D 651 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 406 through 410 removed outlier: 6.832A pdb=" N VAL E 376 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL E 566 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU E 378 " --> pdb=" O VAL E 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 475 through 477 Processing sheet with id=AB4, first strand: chain 'E' and resid 597 through 600 removed outlier: 6.112A pdb=" N THR E 598 " --> pdb=" O CYS E 647 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU E 649 " --> pdb=" O THR E 598 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU E 600 " --> pdb=" O LEU E 649 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ILE E 651 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 406 through 409 removed outlier: 6.364A pdb=" N VAL F 451 " --> pdb=" O ILE F 492 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR F 494 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE F 453 " --> pdb=" O THR F 494 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL F 376 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL F 566 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 378 " --> pdb=" O VAL F 566 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 474 through 477 removed outlier: 4.524A pdb=" N ILE F 484 " --> pdb=" O ARG F 475 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5175 1.34 - 1.48: 3755 1.48 - 1.63: 6967 1.63 - 1.78: 18 1.78 - 1.93: 79 Bond restraints: 15994 Sorted by residual: bond pdb=" O2B AGS B 802 " pdb=" PB AGS B 802 " ideal model delta sigma weight residual 1.531 1.239 0.292 1.60e-02 3.91e+03 3.33e+02 bond pdb=" O2A AGS B 802 " pdb=" PA AGS B 802 " ideal model delta sigma weight residual 1.531 1.264 0.267 1.60e-02 3.91e+03 2.79e+02 bond pdb=" C8 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.370 1.190 0.180 1.10e-02 8.26e+03 2.69e+02 bond pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.374 1.224 0.150 1.00e-02 1.00e+04 2.25e+02 bond pdb=" C3' AGS B 802 " pdb=" C4' AGS B 802 " ideal model delta sigma weight residual 1.526 1.390 0.136 1.10e-02 8.26e+03 1.54e+02 ... (remaining 15989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 21339 4.14 - 8.27: 174 8.27 - 12.41: 21 12.41 - 16.54: 10 16.54 - 20.68: 4 Bond angle restraints: 21548 Sorted by residual: angle pdb=" C4 AGS E 801 " pdb=" N9 AGS E 801 " pdb=" C8 AGS E 801 " ideal model delta sigma weight residual 105.70 115.48 -9.78 4.55e-01 4.83e+00 4.62e+02 angle pdb=" C4 AGS C 802 " pdb=" N9 AGS C 802 " pdb=" C8 AGS C 802 " ideal model delta sigma weight residual 105.70 115.39 -9.69 4.55e-01 4.83e+00 4.53e+02 angle pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " pdb=" C8 AGS B 802 " ideal model delta sigma weight residual 105.70 113.17 -7.47 4.55e-01 4.83e+00 2.70e+02 angle pdb=" N1 AGS B 802 " pdb=" C2 AGS B 802 " pdb=" N3 AGS B 802 " ideal model delta sigma weight residual 128.80 118.57 10.23 8.41e-01 1.41e+00 1.48e+02 angle pdb=" N7 AGS E 801 " pdb=" C8 AGS E 801 " pdb=" N9 AGS E 801 " ideal model delta sigma weight residual 114.03 105.71 8.32 6.99e-01 2.05e+00 1.42e+02 ... (remaining 21543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 9351 25.51 - 51.02: 301 51.02 - 76.54: 47 76.54 - 102.05: 7 102.05 - 127.56: 4 Dihedral angle restraints: 9710 sinusoidal: 4143 harmonic: 5567 Sorted by residual: dihedral pdb=" C4' ADP A 801 " pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -180.00 -52.79 -127.21 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" C2' ADP A 801 " pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C4 ADP A 801 " ideal model delta sinusoidal sigma weight residual 91.55 -143.32 -125.13 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" C VAL B 653 " pdb=" N VAL B 653 " pdb=" CA VAL B 653 " pdb=" CB VAL B 653 " ideal model delta harmonic sigma weight residual -122.00 -134.99 12.99 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 9707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2334 0.384 - 0.768: 3 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.920: 2 Chirality restraints: 2339 Sorted by residual: chirality pdb=" PB AGS B 802 " pdb=" O2B AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O3B AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.26 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" PA AGS B 802 " pdb=" O2A AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O5' AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.56 1.62 2.00e-01 2.50e+01 6.55e+01 chirality pdb=" C2' AGS B 802 " pdb=" C1' AGS B 802 " pdb=" C3' AGS B 802 " pdb=" O2' AGS B 802 " both_signs ideal model delta sigma weight residual False -2.67 -2.02 -0.66 2.00e-01 2.50e+01 1.07e+01 ... (remaining 2336 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 423 " -0.102 2.00e-02 2.50e+03 6.39e-02 7.14e+01 pdb=" CG PHE B 423 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE B 423 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE B 423 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE B 423 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 423 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 423 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AGS D 801 " -0.088 2.00e-02 2.50e+03 4.45e-02 5.44e+01 pdb=" C2 AGS D 801 " 0.041 2.00e-02 2.50e+03 pdb=" C4 AGS D 801 " -0.018 2.00e-02 2.50e+03 pdb=" C5 AGS D 801 " -0.016 2.00e-02 2.50e+03 pdb=" C6 AGS D 801 " -0.006 2.00e-02 2.50e+03 pdb=" C8 AGS D 801 " 0.068 2.00e-02 2.50e+03 pdb=" N1 AGS D 801 " 0.020 2.00e-02 2.50e+03 pdb=" N3 AGS D 801 " -0.002 2.00e-02 2.50e+03 pdb=" N6 AGS D 801 " -0.062 2.00e-02 2.50e+03 pdb=" N7 AGS D 801 " 0.011 2.00e-02 2.50e+03 pdb=" N9 AGS D 801 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 601 " -0.084 2.00e-02 2.50e+03 4.55e-02 5.16e+01 pdb=" CG TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 601 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 601 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 601 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP B 601 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 601 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 601 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 601 " -0.059 2.00e-02 2.50e+03 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 77 2.41 - 3.03: 10282 3.03 - 3.66: 23997 3.66 - 4.28: 37115 4.28 - 4.90: 60810 Nonbonded interactions: 132281 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2G AGS B 802 " model vdw 1.788 2.170 nonbonded pdb=" O1B AGS D 801 " pdb="MG MG D 802 " model vdw 1.905 2.170 nonbonded pdb=" O1A AGS D 801 " pdb="MG MG D 802 " model vdw 2.012 2.170 nonbonded pdb=" OE2 GLU D 455 " pdb="MG MG D 802 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR E 388 " pdb="MG MG E 802 " model vdw 2.161 2.170 ... (remaining 132276 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' and resid 327 through 653) selection = (chain 'B' and (resid 327 through 515 or resid 539 through 653)) selection = (chain 'C' and (resid 327 through 515 or resid 539 through 653)) selection = (chain 'D' and (resid 327 through 515 or resid 539 through 653)) selection = (chain 'E' and (resid 327 through 515 or resid 539 through 653)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.590 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:9.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 0.292 15994 Z= 0.591 Angle : 1.076 20.677 21548 Z= 0.733 Chirality : 0.079 1.920 2339 Planarity : 0.006 0.080 2787 Dihedral : 13.419 127.559 6098 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 0.30 % Allowed : 1.28 % Favored : 98.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1888 helix: 1.46 (0.18), residues: 897 sheet: 0.59 (0.32), residues: 263 loop : 0.31 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 620 TYR 0.075 0.002 TYR A 430 PHE 0.102 0.005 PHE B 423 TRP 0.084 0.004 TRP B 601 HIS 0.012 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.59 (15994) covalent geometry : angle 1.07626 / 0.73 (21548) hydrogen bonds : bond 0.16188 / 11.17 ( 728) hydrogen bonds : angle 7.75242 / 5.79 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 350 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.6650 (tttp) cc_final: 0.6417 (mmtp) REVERT: A 505 HIS cc_start: 0.7331 (m170) cc_final: 0.6927 (m170) REVERT: A 581 ASN cc_start: 0.8261 (m-40) cc_final: 0.7714 (t0) REVERT: A 585 ASN cc_start: 0.8415 (m-40) cc_final: 0.7679 (m-40) REVERT: B 435 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6666 (mt-10) REVERT: B 505 HIS cc_start: 0.6573 (m-70) cc_final: 0.6098 (m-70) REVERT: B 600 LEU cc_start: 0.7858 (mt) cc_final: 0.7645 (mt) REVERT: B 650 ARG cc_start: 0.7987 (mtp85) cc_final: 0.6470 (pmt170) REVERT: C 484 ILE cc_start: 0.7660 (mm) cc_final: 0.7146 (pt) REVERT: C 487 LYS cc_start: 0.7391 (mttt) cc_final: 0.7131 (mttp) REVERT: C 538 LYS cc_start: 0.6853 (mmtt) cc_final: 0.6631 (ptmt) REVERT: C 650 ARG cc_start: 0.6901 (ttp80) cc_final: 0.6643 (ttm170) REVERT: C 658 LYS cc_start: 0.6719 (mtmt) cc_final: 0.6179 (mtpt) REVERT: D 336 ARG cc_start: 0.5222 (mmp80) cc_final: 0.4973 (mmp80) REVERT: D 404 LYS cc_start: 0.7946 (ptmt) cc_final: 0.7430 (pttt) REVERT: D 650 ARG cc_start: 0.6313 (mmt180) cc_final: 0.6084 (ppt170) REVERT: E 337 PHE cc_start: 0.6880 (t80) cc_final: 0.6392 (m-80) REVERT: E 469 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7007 (tt0) REVERT: E 500 ASP cc_start: 0.8506 (m-30) cc_final: 0.8200 (m-30) REVERT: E 554 ARG cc_start: 0.6323 (mtm-85) cc_final: 0.6095 (mtm110) REVERT: E 666 LEU cc_start: 0.7070 (mt) cc_final: 0.6584 (mp) REVERT: F 398 MET cc_start: 0.7398 (mmp) cc_final: 0.7114 (tpt) REVERT: F 410 ASP cc_start: 0.5364 (t0) cc_final: 0.4906 (t70) REVERT: F 458 LYS cc_start: 0.4022 (mttt) cc_final: 0.3774 (mtpt) REVERT: F 493 MET cc_start: 0.6901 (mpp) cc_final: 0.6692 (mpp) REVERT: F 555 ARG cc_start: 0.4315 (ttt180) cc_final: 0.3816 (tmt90) REVERT: F 599 LEU cc_start: 0.6692 (mt) cc_final: 0.6463 (pp) REVERT: F 649 LEU cc_start: 0.7354 (mt) cc_final: 0.7141 (tp) outliers start: 5 outliers final: 4 residues processed: 353 average time/residue: 0.6197 time to fit residues: 238.1172 Evaluate side-chains 171 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain E residue 611 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 HIS A 399 HIS A 563 ASN B 504 GLN C 511 GLN C 595 HIS E 505 HIS F 373 HIS F 624 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104857 restraints weight = 21666.843| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.14 r_work: 0.3149 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15994 Z= 0.165 Angle : 0.634 8.014 21548 Z= 0.323 Chirality : 0.043 0.161 2339 Planarity : 0.005 0.070 2787 Dihedral : 8.765 128.861 2149 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.61 % Allowed : 11.00 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1888 helix: 1.59 (0.18), residues: 905 sheet: 0.44 (0.30), residues: 272 loop : 0.61 (0.27), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 561 TYR 0.018 0.001 TYR A 397 PHE 0.020 0.002 PHE F 558 TRP 0.013 0.001 TRP A 601 HIS 0.010 0.001 HIS F 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (15994) covalent geometry : angle 0.63385 / 0.32 (21548) hydrogen bonds : bond 0.04352 / 2.89 ( 728) hydrogen bonds : angle 6.25775 / 4.73 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7900 (mmtm) REVERT: A 505 HIS cc_start: 0.7081 (m170) cc_final: 0.6846 (m170) REVERT: A 544 VAL cc_start: 0.7549 (m) cc_final: 0.7117 (p) REVERT: A 555 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.7585 (mpt90) REVERT: A 581 ASN cc_start: 0.8436 (m-40) cc_final: 0.7875 (t0) REVERT: A 585 ASN cc_start: 0.8805 (m-40) cc_final: 0.8562 (m-40) REVERT: B 435 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7758 (mt-10) REVERT: B 484 ILE cc_start: 0.8806 (mp) cc_final: 0.8486 (pp) REVERT: B 504 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: B 650 ARG cc_start: 0.8264 (mtp85) cc_final: 0.6723 (pmt170) REVERT: C 348 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8894 (mt) REVERT: C 444 LYS cc_start: 0.8901 (tttp) cc_final: 0.8622 (tttt) REVERT: C 538 LYS cc_start: 0.7410 (mmtt) cc_final: 0.7145 (ptmt) REVERT: C 611 ASP cc_start: 0.8552 (m-30) cc_final: 0.8334 (p0) REVERT: D 404 LYS cc_start: 0.8554 (ptmt) cc_final: 0.8195 (pttt) REVERT: D 575 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8501 (mt-10) REVERT: D 650 ARG cc_start: 0.6531 (mmt180) cc_final: 0.6266 (mmt90) REVERT: E 337 PHE cc_start: 0.7023 (t80) cc_final: 0.6814 (m-80) REVERT: E 554 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.7022 (ptp-110) REVERT: E 650 ARG cc_start: 0.6734 (mmt180) cc_final: 0.6373 (mmp80) REVERT: E 666 LEU cc_start: 0.7731 (mt) cc_final: 0.7383 (mp) REVERT: F 373 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.6392 (t-90) REVERT: F 398 MET cc_start: 0.7086 (mmp) cc_final: 0.6818 (tpt) REVERT: F 410 ASP cc_start: 0.4963 (t0) cc_final: 0.4756 (t70) REVERT: F 416 GLU cc_start: 0.4216 (pm20) cc_final: 0.3851 (tp30) REVERT: F 458 LYS cc_start: 0.3942 (mttt) cc_final: 0.3662 (mtpt) REVERT: F 490 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7018 (mp) REVERT: F 555 ARG cc_start: 0.4321 (ttt180) cc_final: 0.3830 (tmt90) outliers start: 43 outliers final: 14 residues processed: 233 average time/residue: 0.5490 time to fit residues: 140.3182 Evaluate side-chains 167 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain F residue 373 HIS Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN A 596 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 HIS F 632 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106704 restraints weight = 22047.419| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.89 r_work: 0.3156 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15994 Z= 0.148 Angle : 0.587 11.271 21548 Z= 0.298 Chirality : 0.042 0.166 2339 Planarity : 0.004 0.049 2787 Dihedral : 8.275 129.885 2146 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.37 % Allowed : 13.13 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1888 helix: 1.47 (0.18), residues: 910 sheet: 0.30 (0.31), residues: 261 loop : 0.55 (0.26), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 650 TYR 0.018 0.001 TYR A 397 PHE 0.020 0.001 PHE D 540 TRP 0.012 0.001 TRP F 368 HIS 0.016 0.001 HIS F 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15994) covalent geometry : angle 0.58736 / 0.30 (21548) hydrogen bonds : bond 0.03904 / 2.58 ( 728) hydrogen bonds : angle 5.95461 / 4.52 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 337 PHE cc_start: 0.5890 (p90) cc_final: 0.5650 (p90) REVERT: A 398 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7513 (mpt) REVERT: A 487 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8104 (mmtm) REVERT: A 544 VAL cc_start: 0.7560 (m) cc_final: 0.7126 (p) REVERT: A 555 ARG cc_start: 0.7765 (ptp-170) cc_final: 0.7548 (mpt90) REVERT: A 581 ASN cc_start: 0.8470 (m-40) cc_final: 0.7811 (t0) REVERT: A 585 ASN cc_start: 0.8793 (m-40) cc_final: 0.8459 (m-40) REVERT: B 484 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8595 (pp) REVERT: B 589 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8212 (tmtt) REVERT: B 602 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7875 (p0) REVERT: B 650 ARG cc_start: 0.8107 (mtp85) cc_final: 0.6767 (pmt170) REVERT: C 400 LYS cc_start: 0.7403 (mmtt) cc_final: 0.7071 (mppt) REVERT: C 444 LYS cc_start: 0.8994 (tttp) cc_final: 0.8685 (tttt) REVERT: D 404 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8391 (pttm) REVERT: D 435 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8009 (mt-10) REVERT: D 649 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7719 (mt) REVERT: E 413 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: E 554 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7139 (ptp-110) REVERT: E 643 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5622 (pt) REVERT: F 368 TRP cc_start: 0.8255 (m100) cc_final: 0.6810 (m100) REVERT: F 398 MET cc_start: 0.6977 (mmp) cc_final: 0.6725 (tpt) REVERT: F 410 ASP cc_start: 0.5205 (t0) cc_final: 0.4993 (t70) REVERT: F 416 GLU cc_start: 0.4219 (pm20) cc_final: 0.3878 (tp30) REVERT: F 458 LYS cc_start: 0.4117 (mttt) cc_final: 0.3754 (mtpt) REVERT: F 475 ARG cc_start: 0.6781 (mmm-85) cc_final: 0.6268 (tpp-160) REVERT: F 490 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7095 (mp) outliers start: 39 outliers final: 15 residues processed: 196 average time/residue: 0.5027 time to fit residues: 109.4046 Evaluate side-chains 162 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.0030 chunk 187 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 ASN A 496 ASN A 596 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 HIS ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 GLN F 632 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106001 restraints weight = 22055.185| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.24 r_work: 0.3103 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15994 Z= 0.166 Angle : 0.595 16.950 21548 Z= 0.297 Chirality : 0.042 0.181 2339 Planarity : 0.004 0.050 2787 Dihedral : 8.221 130.362 2144 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 3.16 % Allowed : 13.37 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1888 helix: 1.36 (0.17), residues: 907 sheet: 0.17 (0.31), residues: 261 loop : 0.41 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 590 TYR 0.020 0.001 TYR A 397 PHE 0.021 0.001 PHE F 558 TRP 0.009 0.001 TRP F 601 HIS 0.007 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (15994) covalent geometry : angle 0.59469 / 0.30 (21548) hydrogen bonds : bond 0.03830 / 2.54 ( 728) hydrogen bonds : angle 5.80886 / 4.42 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7594 (mpt) REVERT: A 487 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8228 (mmtm) REVERT: A 550 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7048 (mptt) REVERT: A 581 ASN cc_start: 0.8454 (m-40) cc_final: 0.7730 (t0) REVERT: A 585 ASN cc_start: 0.8783 (m-40) cc_final: 0.8460 (m-40) REVERT: A 599 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7687 (pp) REVERT: A 616 HIS cc_start: 0.7686 (p-80) cc_final: 0.7419 (p90) REVERT: A 634 LEU cc_start: 0.8800 (mp) cc_final: 0.8516 (mp) REVERT: B 484 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8668 (pp) REVERT: B 589 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8585 (ttpt) REVERT: B 593 GLN cc_start: 0.8370 (mt0) cc_final: 0.8051 (tp40) REVERT: B 650 ARG cc_start: 0.8078 (mtp85) cc_final: 0.6687 (pmt170) REVERT: C 348 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9023 (mt) REVERT: C 620 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8631 (ptp90) REVERT: D 351 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8568 (mm-30) REVERT: D 404 LYS cc_start: 0.8560 (ptmt) cc_final: 0.8352 (pttm) REVERT: D 435 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8102 (mt-10) REVERT: D 649 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8019 (mt) REVERT: E 413 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: E 454 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8888 (m-30) REVERT: E 554 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7077 (ptp-110) REVERT: E 643 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.5957 (pt) REVERT: E 666 LEU cc_start: 0.7864 (mt) cc_final: 0.7303 (mp) REVERT: F 368 TRP cc_start: 0.8345 (m100) cc_final: 0.6885 (m100) REVERT: F 398 MET cc_start: 0.6985 (mmp) cc_final: 0.6687 (tpt) REVERT: F 410 ASP cc_start: 0.5359 (t0) cc_final: 0.5057 (t70) REVERT: F 416 GLU cc_start: 0.4072 (pm20) cc_final: 0.3839 (tp30) REVERT: F 458 LYS cc_start: 0.4089 (mttt) cc_final: 0.3732 (mtpt) REVERT: F 475 ARG cc_start: 0.6861 (mmm-85) cc_final: 0.6445 (tpp-160) REVERT: F 490 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.6963 (mp) outliers start: 52 outliers final: 18 residues processed: 203 average time/residue: 0.4915 time to fit residues: 111.1539 Evaluate side-chains 171 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 598 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 184 optimal weight: 8.9990 chunk 157 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 181 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 HIS ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN E 504 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS F 624 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.161699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106465 restraints weight = 21957.529| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.17 r_work: 0.3101 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15994 Z= 0.184 Angle : 0.596 12.819 21548 Z= 0.301 Chirality : 0.042 0.166 2339 Planarity : 0.005 0.118 2787 Dihedral : 8.431 129.606 2144 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 2.74 % Allowed : 15.26 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1888 helix: 1.23 (0.17), residues: 907 sheet: 0.03 (0.30), residues: 275 loop : 0.36 (0.26), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 650 TYR 0.021 0.002 TYR A 397 PHE 0.017 0.001 PHE D 540 TRP 0.009 0.001 TRP F 601 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (15994) covalent geometry : angle 0.59616 / 0.30 (21548) hydrogen bonds : bond 0.03817 / 2.54 ( 728) hydrogen bonds : angle 5.78044 / 4.40 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7571 (mpt) REVERT: A 550 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6527 (ttmm) REVERT: A 581 ASN cc_start: 0.8489 (m-40) cc_final: 0.7659 (t0) REVERT: A 585 ASN cc_start: 0.8743 (m-40) cc_final: 0.8395 (m-40) REVERT: A 634 LEU cc_start: 0.8775 (mp) cc_final: 0.8513 (mt) REVERT: B 484 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8596 (pp) REVERT: B 589 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8586 (ttpt) REVERT: B 593 GLN cc_start: 0.8326 (mt0) cc_final: 0.8026 (tp40) REVERT: C 348 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8998 (mt) REVERT: C 400 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7216 (mppt) REVERT: D 351 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: D 404 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8328 (pttm) REVERT: D 435 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8095 (mt-10) REVERT: D 649 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8223 (mt) REVERT: E 413 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: E 454 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8866 (m-30) REVERT: E 554 ARG cc_start: 0.7306 (mtm-85) cc_final: 0.6949 (ptp-110) REVERT: E 643 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6081 (pt) REVERT: E 666 LEU cc_start: 0.7525 (mt) cc_final: 0.7290 (mp) REVERT: F 368 TRP cc_start: 0.8389 (m100) cc_final: 0.6986 (m100) REVERT: F 398 MET cc_start: 0.7008 (mmp) cc_final: 0.6680 (tpt) REVERT: F 410 ASP cc_start: 0.5330 (t0) cc_final: 0.5010 (t70) REVERT: F 416 GLU cc_start: 0.4256 (pm20) cc_final: 0.3972 (tp30) REVERT: F 458 LYS cc_start: 0.4156 (mttt) cc_final: 0.3818 (mtpt) REVERT: F 475 ARG cc_start: 0.6852 (mmm-85) cc_final: 0.6516 (ptt180) REVERT: F 490 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.6937 (mp) outliers start: 45 outliers final: 23 residues processed: 173 average time/residue: 0.5064 time to fit residues: 97.4944 Evaluate side-chains 172 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Chi-restraints excluded: chain F residue 605 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 HIS A 596 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS E 504 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.163149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107372 restraints weight = 21780.508| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.18 r_work: 0.3119 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15994 Z= 0.133 Angle : 0.559 12.116 21548 Z= 0.283 Chirality : 0.041 0.183 2339 Planarity : 0.004 0.068 2787 Dihedral : 8.297 127.832 2144 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.61 % Allowed : 15.26 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1888 helix: 1.30 (0.17), residues: 909 sheet: -0.03 (0.30), residues: 278 loop : 0.45 (0.26), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 650 TYR 0.023 0.001 TYR A 397 PHE 0.015 0.001 PHE D 540 TRP 0.008 0.001 TRP F 601 HIS 0.004 0.001 HIS A 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (15994) covalent geometry : angle 0.55886 / 0.28 (21548) hydrogen bonds : bond 0.03467 / 2.31 ( 728) hydrogen bonds : angle 5.62067 / 4.27 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7532 (mpt) REVERT: A 550 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6977 (ttmm) REVERT: A 581 ASN cc_start: 0.8480 (m-40) cc_final: 0.7726 (t0) REVERT: A 585 ASN cc_start: 0.8717 (m-40) cc_final: 0.8413 (m-40) REVERT: A 634 LEU cc_start: 0.8774 (mp) cc_final: 0.8514 (mt) REVERT: B 554 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7560 (mmt90) REVERT: B 589 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8568 (ttpt) REVERT: B 593 GLN cc_start: 0.8330 (mt0) cc_final: 0.8064 (tp40) REVERT: C 330 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6883 (mp0) REVERT: C 400 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7155 (mppt) REVERT: C 543 ASN cc_start: 0.6175 (m-40) cc_final: 0.5931 (p0) REVERT: D 404 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8352 (pttm) REVERT: D 435 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8094 (mt-10) REVERT: D 508 GLN cc_start: 0.7405 (tt0) cc_final: 0.7123 (tm-30) REVERT: D 640 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7336 (mm-40) REVERT: D 649 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8287 (mt) REVERT: E 413 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: E 454 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8872 (m-30) REVERT: E 554 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.6943 (ptp-110) REVERT: E 643 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.5996 (pt) REVERT: F 368 TRP cc_start: 0.8391 (m100) cc_final: 0.6987 (m100) REVERT: F 398 MET cc_start: 0.6961 (mmp) cc_final: 0.6631 (tpt) REVERT: F 410 ASP cc_start: 0.5381 (t0) cc_final: 0.5012 (t70) REVERT: F 416 GLU cc_start: 0.4318 (pm20) cc_final: 0.4035 (tp30) REVERT: F 458 LYS cc_start: 0.4343 (mttt) cc_final: 0.4000 (mtpt) REVERT: F 475 ARG cc_start: 0.6877 (mmm-85) cc_final: 0.6361 (mtm180) REVERT: F 490 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6913 (mp) outliers start: 43 outliers final: 11 residues processed: 180 average time/residue: 0.5877 time to fit residues: 117.1241 Evaluate side-chains 147 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 105 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 552 HIS B 504 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108264 restraints weight = 21680.729| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.14 r_work: 0.3118 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15994 Z= 0.157 Angle : 0.580 11.325 21548 Z= 0.293 Chirality : 0.041 0.177 2339 Planarity : 0.004 0.054 2787 Dihedral : 8.030 127.309 2142 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 2.07 % Allowed : 16.17 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1888 helix: 1.24 (0.17), residues: 914 sheet: -0.11 (0.30), residues: 279 loop : 0.41 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 650 TYR 0.024 0.001 TYR A 397 PHE 0.031 0.001 PHE F 558 TRP 0.007 0.001 TRP F 601 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (15994) covalent geometry : angle 0.57957 / 0.29 (21548) hydrogen bonds : bond 0.03546 / 2.37 ( 728) hydrogen bonds : angle 5.59807 / 4.26 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7525 (mpt) REVERT: A 550 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7002 (ttmm) REVERT: A 581 ASN cc_start: 0.8474 (m-40) cc_final: 0.7730 (t0) REVERT: A 585 ASN cc_start: 0.8749 (m-40) cc_final: 0.8465 (m-40) REVERT: A 634 LEU cc_start: 0.8780 (mp) cc_final: 0.8526 (mt) REVERT: B 589 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8635 (ttpt) REVERT: B 593 GLN cc_start: 0.8302 (mt0) cc_final: 0.8060 (tp40) REVERT: B 625 GLU cc_start: 0.7755 (tp30) cc_final: 0.7414 (mt-10) REVERT: C 330 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6910 (mp0) REVERT: C 400 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7203 (mppt) REVERT: C 620 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8657 (ptp90) REVERT: D 351 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8525 (mm-30) REVERT: D 435 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8169 (mt-10) REVERT: D 516 MET cc_start: 0.5531 (pmm) cc_final: 0.5265 (pmm) REVERT: D 649 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8294 (mp) REVERT: E 413 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: E 454 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8847 (m-30) REVERT: E 554 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.7006 (ptp-110) REVERT: E 643 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6012 (pt) REVERT: F 368 TRP cc_start: 0.8429 (m100) cc_final: 0.7032 (m100) REVERT: F 398 MET cc_start: 0.6888 (mmp) cc_final: 0.6591 (tpt) REVERT: F 410 ASP cc_start: 0.5510 (t0) cc_final: 0.5125 (t70) REVERT: F 416 GLU cc_start: 0.4414 (pm20) cc_final: 0.4136 (tp30) REVERT: F 458 LYS cc_start: 0.4412 (mttt) cc_final: 0.4039 (mtpt) REVERT: F 490 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6914 (mp) REVERT: F 493 MET cc_start: 0.7069 (mpp) cc_final: 0.6854 (mmt) outliers start: 34 outliers final: 16 residues processed: 165 average time/residue: 0.5934 time to fit residues: 108.2814 Evaluate side-chains 158 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 184 optimal weight: 0.0070 chunk 162 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 552 HIS A 614 ASN B 504 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110353 restraints weight = 21850.549| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.12 r_work: 0.3138 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15994 Z= 0.134 Angle : 0.558 10.989 21548 Z= 0.285 Chirality : 0.040 0.177 2339 Planarity : 0.004 0.048 2787 Dihedral : 7.943 126.413 2142 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.31 % Allowed : 16.05 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1888 helix: 1.28 (0.17), residues: 916 sheet: -0.07 (0.30), residues: 284 loop : 0.46 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 408 TYR 0.026 0.001 TYR A 397 PHE 0.027 0.001 PHE F 558 TRP 0.007 0.001 TRP F 601 HIS 0.010 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (15994) covalent geometry : angle 0.55809 / 0.28 (21548) hydrogen bonds : bond 0.03368 / 2.24 ( 728) hydrogen bonds : angle 5.53611 / 4.20 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7470 (mpt) REVERT: A 550 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7130 (ttmm) REVERT: A 581 ASN cc_start: 0.8469 (m-40) cc_final: 0.7982 (t0) REVERT: A 634 LEU cc_start: 0.8794 (mp) cc_final: 0.8532 (mt) REVERT: B 554 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7635 (mmt90) REVERT: B 589 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8626 (ttpt) REVERT: B 593 GLN cc_start: 0.8301 (mt0) cc_final: 0.8022 (tp40) REVERT: B 611 ASP cc_start: 0.8088 (t70) cc_final: 0.7797 (m-30) REVERT: B 625 GLU cc_start: 0.7725 (tp30) cc_final: 0.7450 (mt-10) REVERT: C 330 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6940 (mp0) REVERT: C 400 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7169 (mppt) REVERT: C 484 ILE cc_start: 0.8797 (mp) cc_final: 0.8540 (pp) REVERT: C 620 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8623 (ptp90) REVERT: D 351 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8511 (mm-30) REVERT: D 435 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8178 (mt-10) REVERT: D 511 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8046 (mt0) REVERT: D 649 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8300 (mp) REVERT: E 413 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: E 454 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8844 (m-30) REVERT: E 554 ARG cc_start: 0.7256 (mtm-85) cc_final: 0.6953 (ptp-110) REVERT: E 643 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5917 (pt) REVERT: E 661 LEU cc_start: 0.4368 (OUTLIER) cc_final: 0.4118 (mm) REVERT: F 368 TRP cc_start: 0.8410 (m100) cc_final: 0.6995 (m100) REVERT: F 398 MET cc_start: 0.6971 (mmp) cc_final: 0.6696 (tpt) REVERT: F 410 ASP cc_start: 0.5415 (t0) cc_final: 0.5054 (t70) REVERT: F 416 GLU cc_start: 0.4431 (pm20) cc_final: 0.4079 (tp30) REVERT: F 458 LYS cc_start: 0.4438 (mttt) cc_final: 0.4096 (mtpt) REVERT: F 490 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6923 (mp) outliers start: 38 outliers final: 16 residues processed: 169 average time/residue: 0.5607 time to fit residues: 104.9892 Evaluate side-chains 161 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 623 LYS Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 657 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 471 PHE Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 169 optimal weight: 0.0060 chunk 100 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.163331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107750 restraints weight = 21834.088| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.42 r_work: 0.3108 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15994 Z= 0.133 Angle : 0.563 10.785 21548 Z= 0.286 Chirality : 0.040 0.174 2339 Planarity : 0.004 0.055 2787 Dihedral : 7.892 125.858 2142 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 1.88 % Allowed : 16.96 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1888 helix: 1.28 (0.17), residues: 921 sheet: -0.09 (0.30), residues: 284 loop : 0.48 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 650 TYR 0.026 0.001 TYR A 397 PHE 0.025 0.001 PHE F 558 TRP 0.010 0.001 TRP A 601 HIS 0.014 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (15994) covalent geometry : angle 0.56297 / 0.29 (21548) hydrogen bonds : bond 0.03335 / 2.23 ( 728) hydrogen bonds : angle 5.46573 / 4.15 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7492 (mpt) REVERT: A 550 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7082 (ttmm) REVERT: A 634 LEU cc_start: 0.8780 (mp) cc_final: 0.8556 (mt) REVERT: B 554 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7768 (mmt90) REVERT: B 589 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8577 (ttpt) REVERT: B 593 GLN cc_start: 0.8341 (mt0) cc_final: 0.8035 (tp40) REVERT: B 611 ASP cc_start: 0.8142 (t70) cc_final: 0.7804 (m-30) REVERT: B 625 GLU cc_start: 0.7731 (tp30) cc_final: 0.7438 (mt-10) REVERT: C 400 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7162 (mppt) REVERT: C 484 ILE cc_start: 0.8817 (mp) cc_final: 0.8512 (pp) REVERT: C 620 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8623 (ptp90) REVERT: D 351 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: D 435 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8193 (mt-10) REVERT: D 508 GLN cc_start: 0.7425 (tt0) cc_final: 0.7129 (tm-30) REVERT: D 511 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8076 (mt0) REVERT: D 649 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8316 (mp) REVERT: E 413 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: E 454 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8855 (m-30) REVERT: E 554 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6872 (ptp-110) REVERT: E 643 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5938 (pt) REVERT: E 661 LEU cc_start: 0.4457 (OUTLIER) cc_final: 0.4146 (mm) REVERT: F 368 TRP cc_start: 0.8408 (m100) cc_final: 0.7166 (m100) REVERT: F 398 MET cc_start: 0.7091 (mmp) cc_final: 0.6776 (tpt) REVERT: F 410 ASP cc_start: 0.5326 (t0) cc_final: 0.4949 (t70) REVERT: F 416 GLU cc_start: 0.4298 (pm20) cc_final: 0.4059 (tp30) REVERT: F 458 LYS cc_start: 0.4291 (mttt) cc_final: 0.3929 (mtpt) REVERT: F 490 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6885 (mp) outliers start: 31 outliers final: 11 residues processed: 163 average time/residue: 0.5379 time to fit residues: 97.7167 Evaluate side-chains 155 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 657 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 0.0270 chunk 11 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 chunk 172 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS C 539 ASN C 543 ASN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.164297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110431 restraints weight = 21789.121| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.40 r_work: 0.3130 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15994 Z= 0.115 Angle : 0.553 11.015 21548 Z= 0.282 Chirality : 0.040 0.176 2339 Planarity : 0.004 0.055 2787 Dihedral : 7.783 125.009 2142 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 1.52 % Allowed : 17.45 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1888 helix: 1.40 (0.17), residues: 916 sheet: -0.15 (0.29), residues: 293 loop : 0.51 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 650 TYR 0.028 0.001 TYR A 397 PHE 0.024 0.001 PHE F 558 TRP 0.007 0.001 TRP F 601 HIS 0.013 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15994) covalent geometry : angle 0.55259 / 0.28 (21548) hydrogen bonds : bond 0.03149 / 2.10 ( 728) hydrogen bonds : angle 5.37791 / 4.08 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7449 (mpt) REVERT: A 550 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7132 (ttmm) REVERT: A 634 LEU cc_start: 0.8771 (mp) cc_final: 0.8569 (mt) REVERT: B 554 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7736 (mmt90) REVERT: B 589 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8533 (ttpt) REVERT: B 593 GLN cc_start: 0.8340 (mt0) cc_final: 0.8005 (tp40) REVERT: B 611 ASP cc_start: 0.8105 (t70) cc_final: 0.7761 (m-30) REVERT: C 400 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7146 (mppt) REVERT: C 484 ILE cc_start: 0.8754 (mp) cc_final: 0.8508 (pp) REVERT: C 620 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8594 (ptp90) REVERT: D 435 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8190 (mt-10) REVERT: D 508 GLN cc_start: 0.7415 (tt0) cc_final: 0.7121 (tm-30) REVERT: D 511 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8083 (mt0) REVERT: E 413 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: E 454 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8783 (m-30) REVERT: E 554 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6866 (ptp-110) REVERT: E 643 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.5944 (pt) REVERT: E 661 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.4155 (mm) REVERT: F 368 TRP cc_start: 0.8405 (m100) cc_final: 0.7417 (m100) REVERT: F 398 MET cc_start: 0.7097 (mmp) cc_final: 0.6783 (tpt) REVERT: F 410 ASP cc_start: 0.5338 (t0) cc_final: 0.4967 (t70) REVERT: F 416 GLU cc_start: 0.4342 (pm20) cc_final: 0.4128 (tp30) REVERT: F 458 LYS cc_start: 0.4389 (mttt) cc_final: 0.4016 (mtpt) REVERT: F 490 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6914 (mp) outliers start: 25 outliers final: 9 residues processed: 155 average time/residue: 0.5623 time to fit residues: 97.0545 Evaluate side-chains 147 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 620 ARG Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 657 ASP Chi-restraints excluded: chain E residue 413 GLU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 490 ILE Chi-restraints excluded: chain F residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 174 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.162450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109127 restraints weight = 21636.008| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.10 r_work: 0.3108 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15994 Z= 0.164 Angle : 0.587 10.779 21548 Z= 0.297 Chirality : 0.041 0.175 2339 Planarity : 0.004 0.056 2787 Dihedral : 7.864 125.947 2142 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 1.46 % Allowed : 17.87 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1888 helix: 1.27 (0.17), residues: 920 sheet: -0.23 (0.29), residues: 289 loop : 0.37 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 650 TYR 0.028 0.001 TYR A 397 PHE 0.022 0.001 PHE F 558 TRP 0.008 0.001 TRP B 587 HIS 0.015 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (15994) covalent geometry : angle 0.58676 / 0.30 (21548) hydrogen bonds : bond 0.03494 / 2.33 ( 728) hydrogen bonds : angle 5.46808 / 4.16 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5789.10 seconds wall clock time: 99 minutes 16.89 seconds (5956.89 seconds total)