Starting phenix.real_space_refine on Sat Jun 14 11:01:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ttr_26121/06_2025/7ttr_26121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ttr_26121/06_2025/7ttr_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_26121/06_2025/7ttr_26121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ttr_26121/06_2025/7ttr_26121.map" model { file = "/net/cci-nas-00/data/ceres_data/7ttr_26121/06_2025/7ttr_26121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ttr_26121/06_2025/7ttr_26121.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.13, per 1000 atoms: 0.65 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: 4.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.86 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: 4.93 Time building geometry restraints manager: 4.76 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: 9367 25.51 - 51.02: 318 51.02 - 76.54: 58 76.54 - 102.05: 7 102.05 - 127.56: 4 Dihedral angle restraints: 9754 sinusoidal: 4187 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 9751 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: 2.510 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: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.900 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 13.731 127.559 6142 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), 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 TRP 0.084 0.004 TRP B 601 HIS 0.012 0.001 HIS B 418 PHE 0.102 0.005 PHE B 423 TYR 0.075 0.002 TYR A 430 ARG 0.009 0.000 ARG D 620 Details of bonding type rmsd hydrogen bonds : bond 0.16188 ( 728) hydrogen bonds : angle 7.75242 ( 2100) covalent geometry : bond 0.00906 (15994) covalent geometry : angle 1.07626 (21548) *********************** 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 : 1.686 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: 0.6930 (m170) REVERT: A 581 ASN cc_start: 0.8261 (m-40) cc_final: 0.7724 (t0) REVERT: A 585 ASN cc_start: 0.8415 (m-40) cc_final: 0.7686 (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: 0.7646 (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: 0.6415 (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: 0.7113 (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: 1.6179 time to fit residues: 624.0968 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 : 1.830 ------------------------------------------------------------------------------- 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 160 optimal weight: 0.0980 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS A 399 HIS A 563 ASN B 504 GLN C 511 GLN E 505 HIS F 373 HIS F 418 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 = 0.4106 r_free = 0.4106 target = 0.165232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107805 restraints weight = 21724.173| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.46 r_work: 0.3165 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15994 Z= 0.149 Angle : 0.614 7.790 21548 Z= 0.316 Chirality : 0.042 0.165 2339 Planarity : 0.005 0.083 2787 Dihedral : 9.954 128.945 2193 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 2.37 % Allowed : 11.19 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 1888 helix: 1.66 (0.18), residues: 908 sheet: 0.46 (0.30), residues: 272 loop : 0.67 (0.27), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 601 HIS 0.010 0.001 HIS F 373 PHE 0.020 0.002 PHE F 558 TYR 0.017 0.001 TYR A 397 ARG 0.014 0.001 ARG F 561 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 728) hydrogen bonds : angle 6.28252 ( 2100) covalent geometry : bond 0.00336 (15994) covalent geometry : angle 0.61416 (21548) *********************** 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 240 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 2.037 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7834 (mmtm) REVERT: A 505 HIS cc_start: 0.7089 (m170) cc_final: 0.6806 (m170) REVERT: A 544 VAL cc_start: 0.7516 (m) cc_final: 0.7095 (p) REVERT: A 555 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7587 (mpt90) REVERT: A 581 ASN cc_start: 0.8441 (m-40) cc_final: 0.8040 (t0) REVERT: B 369 TYR cc_start: 0.8175 (p90) cc_final: 0.7927 (p90) REVERT: B 435 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7753 (mt-10) REVERT: B 484 ILE cc_start: 0.8807 (mp) cc_final: 0.8538 (pp) REVERT: B 504 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: B 650 ARG cc_start: 0.8250 (mtp85) cc_final: 0.6666 (pmt170) REVERT: C 348 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8901 (mt) REVERT: C 444 LYS cc_start: 0.8837 (tttp) cc_final: 0.8554 (tttt) REVERT: C 538 LYS cc_start: 0.7433 (mmtt) cc_final: 0.7181 (ptmt) REVERT: C 611 ASP cc_start: 0.8587 (m-30) cc_final: 0.8340 (p0) REVERT: D 404 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8212 (pttt) REVERT: D 575 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8456 (mt-10) REVERT: D 650 ARG cc_start: 0.6495 (mmt180) cc_final: 0.6207 (mmt90) REVERT: E 337 PHE cc_start: 0.7103 (t80) cc_final: 0.6863 (m-80) REVERT: E 554 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6873 (ptp-110) REVERT: E 650 ARG cc_start: 0.6687 (mmt180) cc_final: 0.6320 (mmp80) REVERT: E 666 LEU cc_start: 0.7679 (mt) cc_final: 0.7323 (mp) REVERT: F 373 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6401 (t-90) REVERT: F 398 MET cc_start: 0.7054 (mmp) cc_final: 0.6806 (tpt) REVERT: F 416 GLU cc_start: 0.4256 (pm20) cc_final: 0.3806 (tp30) REVERT: F 458 LYS cc_start: 0.3978 (mttt) cc_final: 0.3737 (mtpt) REVERT: F 490 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7051 (mp) REVERT: F 555 ARG cc_start: 0.4298 (ttt180) cc_final: 0.3726 (tmt90) outliers start: 39 outliers final: 15 residues processed: 231 average time/residue: 1.6879 time to fit residues: 428.1934 Evaluate side-chains 170 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 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 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 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 454 ASP 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 63 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 68 optimal weight: 0.1980 chunk 189 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 C 595 HIS F 632 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110082 restraints weight = 21877.783| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.23 r_work: 0.3164 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2795 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= 0.126 Angle : 0.575 11.059 21548 Z= 0.293 Chirality : 0.041 0.173 2339 Planarity : 0.004 0.048 2787 Dihedral : 9.527 129.486 2190 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 2.31 % Allowed : 13.43 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.21), residues: 1888 helix: 1.55 (0.18), residues: 912 sheet: 0.32 (0.31), residues: 261 loop : 0.67 (0.27), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 368 HIS 0.010 0.001 HIS F 373 PHE 0.019 0.001 PHE D 540 TYR 0.015 0.001 TYR A 397 ARG 0.006 0.000 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 728) hydrogen bonds : angle 5.91592 ( 2100) covalent geometry : bond 0.00288 (15994) covalent geometry : angle 0.57468 (21548) *********************** 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: 38 poor density : 169 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 398 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7437 (mpt) REVERT: A 487 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8104 (mmtm) REVERT: A 544 VAL cc_start: 0.7588 (m) cc_final: 0.7163 (p) REVERT: A 555 ARG cc_start: 0.7787 (ptp-170) cc_final: 0.7577 (mpt90) REVERT: B 589 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8194 (tmtt) REVERT: B 602 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7910 (p0) REVERT: B 650 ARG cc_start: 0.8128 (mtp85) cc_final: 0.6790 (pmt170) REVERT: C 400 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7076 (mppt) REVERT: C 444 LYS cc_start: 0.8997 (tttp) cc_final: 0.8704 (tttt) REVERT: C 484 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8501 (pp) REVERT: D 404 LYS cc_start: 0.8629 (ptmt) cc_final: 0.8380 (pttt) REVERT: D 649 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7665 (mt) REVERT: E 454 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8888 (m-30) REVERT: E 554 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7163 (ptp-110) REVERT: E 643 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5568 (pt) REVERT: E 650 ARG cc_start: 0.6816 (mmt180) cc_final: 0.6581 (mmp80) REVERT: F 368 TRP cc_start: 0.8250 (m100) cc_final: 0.6764 (m100) REVERT: F 398 MET cc_start: 0.6994 (mmp) cc_final: 0.6731 (tpt) REVERT: F 416 GLU cc_start: 0.4357 (pm20) cc_final: 0.3906 (tp30) REVERT: F 458 LYS cc_start: 0.4194 (mttt) cc_final: 0.3828 (mtpt) REVERT: F 490 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7147 (mp) outliers start: 38 outliers final: 10 residues processed: 198 average time/residue: 1.5519 time to fit residues: 337.9920 Evaluate side-chains 153 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 630 VAL 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 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 D residue 649 LEU Chi-restraints excluded: chain D residue 660 LEU 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 558 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 596 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN C 552 HIS ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 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 = 0.4040 r_free = 0.4040 target = 0.160605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103278 restraints weight = 21782.682| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.40 r_work: 0.3057 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 15994 Z= 0.259 Angle : 0.666 15.929 21548 Z= 0.332 Chirality : 0.045 0.172 2339 Planarity : 0.005 0.049 2787 Dihedral : 9.873 136.745 2188 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 2.86 % Allowed : 14.10 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1888 helix: 1.22 (0.17), residues: 905 sheet: 0.21 (0.31), residues: 261 loop : 0.32 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 587 HIS 0.018 0.001 HIS B 505 PHE 0.027 0.002 PHE E 568 TYR 0.019 0.002 TYR A 397 ARG 0.006 0.001 ARG D 620 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 728) hydrogen bonds : angle 5.96958 ( 2100) covalent geometry : bond 0.00637 (15994) covalent geometry : angle 0.66649 (21548) *********************** 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 204 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7637 (mpt) REVERT: A 487 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8214 (mmtm) REVERT: A 599 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7736 (pp) REVERT: A 616 HIS cc_start: 0.7668 (p-80) cc_final: 0.7330 (p90) REVERT: A 634 LEU cc_start: 0.8805 (mp) cc_final: 0.8546 (mt) REVERT: B 589 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8272 (tmtt) REVERT: B 611 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8076 (t0) REVERT: B 650 ARG cc_start: 0.8133 (mtp85) cc_final: 0.6692 (pmt170) REVERT: C 348 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8967 (mt) REVERT: C 444 LYS cc_start: 0.9039 (tttp) cc_final: 0.8798 (tttt) REVERT: D 351 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8562 (mm-30) REVERT: D 404 LYS cc_start: 0.8557 (ptmt) cc_final: 0.8343 (pttm) REVERT: D 649 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7951 (mt) REVERT: D 658 LYS cc_start: 0.7611 (tptp) cc_final: 0.7194 (mttt) REVERT: E 413 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: E 554 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.7127 (ptp-110) REVERT: E 643 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.5928 (pt) REVERT: E 650 ARG cc_start: 0.6779 (mmt180) cc_final: 0.6577 (mmp80) REVERT: E 666 LEU cc_start: 0.7931 (mt) cc_final: 0.7500 (mp) REVERT: F 368 TRP cc_start: 0.8360 (m100) cc_final: 0.6932 (m100) REVERT: F 398 MET cc_start: 0.6962 (mmp) cc_final: 0.6628 (tpt) REVERT: F 416 GLU cc_start: 0.4203 (pm20) cc_final: 0.3869 (tp30) REVERT: F 458 LYS cc_start: 0.4190 (mttt) cc_final: 0.3829 (mtpt) REVERT: F 475 ARG cc_start: 0.6452 (mmt-90) cc_final: 0.5992 (tpp-160) REVERT: F 490 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.6930 (mp) outliers start: 47 outliers final: 21 residues processed: 189 average time/residue: 1.3890 time to fit residues: 295.9129 Evaluate side-chains 170 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 465 THR 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 599 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 611 ASP 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 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 504 GLN 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 128 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 496 ASN A 581 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN C 552 HIS D 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111579 restraints weight = 22049.055| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.27 r_work: 0.3138 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15994 Z= 0.123 Angle : 0.554 12.872 21548 Z= 0.282 Chirality : 0.040 0.159 2339 Planarity : 0.004 0.049 2787 Dihedral : 9.697 131.387 2188 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 2.43 % Allowed : 15.14 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1888 helix: 1.29 (0.17), residues: 911 sheet: 0.08 (0.30), residues: 274 loop : 0.47 (0.26), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 601 HIS 0.004 0.001 HIS F 399 PHE 0.018 0.001 PHE D 540 TYR 0.021 0.001 TYR A 397 ARG 0.004 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 728) hydrogen bonds : angle 5.68245 ( 2100) covalent geometry : bond 0.00286 (15994) covalent geometry : angle 0.55448 (21548) *********************** 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 195 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7656 (mpt) REVERT: A 487 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8208 (mmtm) REVERT: A 550 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6545 (ttmm) REVERT: A 590 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6545 (tmm-80) REVERT: A 599 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 616 HIS cc_start: 0.7719 (p-80) cc_final: 0.7515 (p90) REVERT: A 634 LEU cc_start: 0.8766 (mp) cc_final: 0.8544 (mt) REVERT: B 400 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7225 (ptpt) REVERT: B 589 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8631 (ttpt) REVERT: B 593 GLN cc_start: 0.8373 (mt0) cc_final: 0.8084 (tp40) REVERT: B 650 ARG cc_start: 0.8041 (mtp85) cc_final: 0.6644 (pmt170) REVERT: C 400 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7169 (mppt) REVERT: C 543 ASN cc_start: 0.6093 (m-40) cc_final: 0.5880 (p0) REVERT: D 404 LYS cc_start: 0.8616 (ptmt) cc_final: 0.8413 (pttm) REVERT: D 649 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7967 (mt) REVERT: E 454 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8857 (m-30) REVERT: E 554 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.7092 (ptp-110) REVERT: E 643 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6020 (pt) REVERT: E 666 LEU cc_start: 0.7926 (mt) cc_final: 0.7382 (mp) REVERT: F 368 TRP cc_start: 0.8394 (m100) cc_final: 0.6993 (m100) REVERT: F 398 MET cc_start: 0.6880 (mmp) cc_final: 0.6625 (tpt) REVERT: F 416 GLU cc_start: 0.4261 (pm20) cc_final: 0.3953 (tp30) REVERT: F 458 LYS cc_start: 0.4186 (mttt) cc_final: 0.3837 (mtpt) REVERT: F 475 ARG cc_start: 0.6414 (mmt-90) cc_final: 0.5445 (ttm170) REVERT: F 490 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7053 (mp) outliers start: 40 outliers final: 19 residues processed: 183 average time/residue: 1.4597 time to fit residues: 295.5753 Evaluate side-chains 161 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 590 ARG 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 B residue 400 LYS 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 661 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 504 GLN 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 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 159 optimal weight: 20.0000 chunk 2 optimal weight: 0.0870 chunk 160 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 HIS A 573 HIS A 581 ASN A 596 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS ** F 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.164095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112968 restraints weight = 21952.465| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.06 r_work: 0.3160 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3599 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= 0.118 Angle : 0.552 11.834 21548 Z= 0.280 Chirality : 0.040 0.187 2339 Planarity : 0.004 0.050 2787 Dihedral : 9.351 130.202 2186 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 2.61 % Allowed : 15.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1888 helix: 1.34 (0.17), residues: 915 sheet: -0.01 (0.31), residues: 273 loop : 0.56 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 601 HIS 0.007 0.001 HIS A 505 PHE 0.014 0.001 PHE D 540 TYR 0.023 0.001 TYR A 397 ARG 0.004 0.000 ARG F 475 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 728) hydrogen bonds : angle 5.55303 ( 2100) covalent geometry : bond 0.00274 (15994) covalent geometry : angle 0.55161 (21548) *********************** 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 185 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7583 (mpt) REVERT: A 487 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8252 (mmtm) REVERT: A 550 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.7135 (ttmm) REVERT: A 599 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7785 (pp) REVERT: A 634 LEU cc_start: 0.8777 (mp) cc_final: 0.8575 (mt) REVERT: B 589 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8633 (ttpt) REVERT: B 593 GLN cc_start: 0.8297 (mt0) cc_final: 0.8057 (tp40) REVERT: C 400 LYS cc_start: 0.7469 (mmtt) cc_final: 0.7165 (mppt) REVERT: C 484 ILE cc_start: 0.8774 (mp) cc_final: 0.8532 (pp) REVERT: C 620 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8614 (ptp90) REVERT: D 508 GLN cc_start: 0.7473 (tt0) cc_final: 0.7210 (tm-30) REVERT: D 649 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8115 (mt) REVERT: E 454 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8830 (m-30) REVERT: E 554 ARG cc_start: 0.7225 (mtm-85) cc_final: 0.6978 (ptp-110) REVERT: E 643 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6023 (pt) REVERT: E 666 LEU cc_start: 0.7583 (mt) cc_final: 0.7362 (mp) REVERT: F 368 TRP cc_start: 0.8390 (m100) cc_final: 0.6995 (m100) REVERT: F 398 MET cc_start: 0.6820 (mmp) cc_final: 0.6591 (tpt) REVERT: F 416 GLU cc_start: 0.4251 (pm20) cc_final: 0.3977 (tp30) REVERT: F 458 LYS cc_start: 0.4181 (mttt) cc_final: 0.3827 (mtpt) REVERT: F 490 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6956 (mp) REVERT: F 493 MET cc_start: 0.7102 (mpp) cc_final: 0.6806 (mmt) outliers start: 43 outliers final: 15 residues processed: 174 average time/residue: 1.4114 time to fit residues: 275.0598 Evaluate side-chains 150 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 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 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 666 LEU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 504 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 HIS A 573 HIS A 581 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 552 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 HIS ** F 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.162926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111153 restraints weight = 21928.482| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.14 r_work: 0.3134 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3724 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= 0.147 Angle : 0.565 11.079 21548 Z= 0.286 Chirality : 0.041 0.162 2339 Planarity : 0.004 0.050 2787 Dihedral : 9.334 130.273 2186 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.13 % Rotamer: Outliers : 2.19 % Allowed : 16.29 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1888 helix: 1.35 (0.17), residues: 908 sheet: -0.01 (0.31), residues: 273 loop : 0.50 (0.26), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 601 HIS 0.010 0.001 HIS A 505 PHE 0.032 0.001 PHE F 558 TYR 0.024 0.001 TYR A 397 ARG 0.004 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 728) hydrogen bonds : angle 5.55460 ( 2100) covalent geometry : bond 0.00353 (15994) covalent geometry : angle 0.56471 (21548) *********************** 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 169 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7533 (mpt) REVERT: A 599 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 634 LEU cc_start: 0.8791 (mp) cc_final: 0.8550 (mt) REVERT: B 554 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7564 (mmt90) REVERT: B 589 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8645 (ttpt) REVERT: B 593 GLN cc_start: 0.8281 (mt0) cc_final: 0.8000 (tp40) REVERT: C 400 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7193 (mppt) REVERT: C 484 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8523 (pp) REVERT: C 620 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8640 (ptp90) REVERT: D 508 GLN cc_start: 0.7452 (tt0) cc_final: 0.7179 (tm-30) REVERT: D 516 MET cc_start: 0.5511 (pmm) cc_final: 0.5241 (pmm) REVERT: D 649 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8239 (mt) REVERT: E 454 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8843 (m-30) REVERT: E 643 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6046 (pt) REVERT: F 368 TRP cc_start: 0.8422 (m100) cc_final: 0.7009 (m100) REVERT: F 398 MET cc_start: 0.6846 (mmp) cc_final: 0.6570 (tpt) REVERT: F 416 GLU cc_start: 0.4290 (pm20) cc_final: 0.4002 (tp30) REVERT: F 458 LYS cc_start: 0.4226 (mttt) cc_final: 0.3864 (mtpt) REVERT: F 490 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6926 (mp) outliers start: 36 outliers final: 18 residues processed: 157 average time/residue: 1.6487 time to fit residues: 288.9290 Evaluate side-chains 154 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 599 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 504 GLN 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 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 661 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain D residue 352 SER 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 454 ASP Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 643 LEU 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 134 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 HIS A 581 ASN A 585 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 552 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111241 restraints weight = 21719.041| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.10 r_work: 0.3148 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3793 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= 0.126 Angle : 0.545 10.818 21548 Z= 0.277 Chirality : 0.040 0.163 2339 Planarity : 0.004 0.050 2787 Dihedral : 9.197 129.296 2186 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 1.88 % Allowed : 16.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1888 helix: 1.34 (0.17), residues: 917 sheet: 0.01 (0.31), residues: 278 loop : 0.57 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 601 HIS 0.009 0.001 HIS A 552 PHE 0.026 0.001 PHE F 558 TYR 0.025 0.001 TYR A 397 ARG 0.003 0.000 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 728) hydrogen bonds : angle 5.47962 ( 2100) covalent geometry : bond 0.00297 (15994) covalent geometry : angle 0.54521 (21548) *********************** 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 169 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7510 (mpt) REVERT: A 487 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8201 (mmtm) REVERT: A 585 ASN cc_start: 0.8180 (m-40) cc_final: 0.7978 (m-40) REVERT: B 554 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7557 (mmt90) REVERT: B 589 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8606 (ttpt) REVERT: B 593 GLN cc_start: 0.8292 (mt0) cc_final: 0.8020 (tp40) REVERT: C 400 LYS cc_start: 0.7473 (mmtt) cc_final: 0.7143 (mppt) REVERT: C 484 ILE cc_start: 0.8795 (mp) cc_final: 0.8523 (pp) REVERT: C 620 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8607 (ptp90) REVERT: D 508 GLN cc_start: 0.7398 (tt0) cc_final: 0.7146 (tm-30) REVERT: D 511 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8039 (mt0) REVERT: D 649 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (mt) REVERT: E 454 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8836 (m-30) REVERT: E 643 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6079 (pt) REVERT: F 368 TRP cc_start: 0.8416 (m100) cc_final: 0.7147 (m100) REVERT: F 398 MET cc_start: 0.6887 (mmp) cc_final: 0.6622 (tpt) REVERT: F 416 GLU cc_start: 0.4313 (pm20) cc_final: 0.4044 (tp30) REVERT: F 458 LYS cc_start: 0.4376 (mttt) cc_final: 0.4035 (mtpt) REVERT: F 490 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.6895 (mp) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 1.2257 time to fit residues: 219.2554 Evaluate side-chains 152 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 504 GLN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 504 GLN 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 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 500 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 493 MET Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 643 LEU 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 79 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 34 optimal weight: 0.0470 chunk 171 optimal weight: 6.9990 chunk 136 optimal weight: 0.0770 chunk 137 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 614 ASN A 616 HIS B 552 HIS ** 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 = 0.4075 r_free = 0.4075 target = 0.163872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109213 restraints weight = 21774.021| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.13 r_work: 0.3135 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15994 Z= 0.127 Angle : 0.554 10.830 21548 Z= 0.280 Chirality : 0.040 0.174 2339 Planarity : 0.004 0.050 2787 Dihedral : 9.151 128.992 2186 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 1.95 % Allowed : 16.60 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1888 helix: 1.37 (0.17), residues: 915 sheet: -0.02 (0.31), residues: 278 loop : 0.55 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 601 HIS 0.010 0.001 HIS B 505 PHE 0.023 0.001 PHE F 558 TYR 0.026 0.001 TYR A 397 ARG 0.003 0.000 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 728) hydrogen bonds : angle 5.46129 ( 2100) covalent geometry : bond 0.00301 (15994) covalent geometry : angle 0.55353 (21548) *********************** 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 170 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7440 (mpt) REVERT: A 487 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8173 (mmtm) REVERT: A 585 ASN cc_start: 0.8204 (m-40) cc_final: 0.7987 (m110) REVERT: A 634 LEU cc_start: 0.8661 (mt) cc_final: 0.8292 (mp) REVERT: B 554 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7570 (mmt90) REVERT: B 589 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8569 (ttpt) REVERT: B 593 GLN cc_start: 0.8302 (mt0) cc_final: 0.8003 (tp40) REVERT: C 330 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6872 (mp0) REVERT: C 400 LYS cc_start: 0.7484 (mmtt) cc_final: 0.7132 (mppt) REVERT: C 484 ILE cc_start: 0.8802 (mp) cc_final: 0.8512 (pp) REVERT: C 620 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8601 (ptp90) REVERT: C 625 GLU cc_start: 0.8581 (tp30) cc_final: 0.8320 (tp30) REVERT: D 508 GLN cc_start: 0.7369 (tt0) cc_final: 0.7093 (tm-30) REVERT: D 511 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8056 (mt0) REVERT: D 649 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8285 (mt) REVERT: E 454 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8847 (m-30) REVERT: E 643 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6142 (pt) REVERT: F 368 TRP cc_start: 0.8444 (m100) cc_final: 0.7136 (m100) REVERT: F 398 MET cc_start: 0.6971 (mmp) cc_final: 0.6698 (tpt) REVERT: F 416 GLU cc_start: 0.4305 (pm20) cc_final: 0.4047 (tp30) REVERT: F 458 LYS cc_start: 0.4413 (mttt) cc_final: 0.4062 (mtpt) REVERT: F 490 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6947 (mp) outliers start: 32 outliers final: 17 residues processed: 159 average time/residue: 1.2036 time to fit residues: 213.5479 Evaluate side-chains 155 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 497 VAL Chi-restraints excluded: chain A residue 504 GLN 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 641 ASP 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 661 LEU 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 454 ASP Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 643 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 73 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 79 optimal weight: 4.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4077 r_free = 0.4077 target = 0.163873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112834 restraints weight = 21911.880| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.12 r_work: 0.3145 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3967 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= 0.125 Angle : 0.551 10.927 21548 Z= 0.280 Chirality : 0.040 0.176 2339 Planarity : 0.004 0.049 2787 Dihedral : 9.098 128.253 2186 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 1.76 % Allowed : 16.84 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1888 helix: 1.38 (0.17), residues: 917 sheet: -0.11 (0.31), residues: 284 loop : 0.55 (0.26), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 601 HIS 0.008 0.001 HIS A 505 PHE 0.024 0.001 PHE F 558 TYR 0.027 0.001 TYR A 397 ARG 0.003 0.000 ARG B 510 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 728) hydrogen bonds : angle 5.42279 ( 2100) covalent geometry : bond 0.00298 (15994) covalent geometry : angle 0.55137 (21548) ********************** 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 165 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7519 (mpt) REVERT: A 487 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8241 (mmtm) REVERT: A 634 LEU cc_start: 0.8658 (mt) cc_final: 0.8348 (mp) REVERT: B 554 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7714 (mmt90) REVERT: B 589 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8574 (ttpt) REVERT: B 593 GLN cc_start: 0.8222 (mt0) cc_final: 0.7981 (tp40) REVERT: B 611 ASP cc_start: 0.7898 (t0) cc_final: 0.7657 (m-30) REVERT: C 400 LYS cc_start: 0.7499 (mmtt) cc_final: 0.7181 (mppt) REVERT: C 484 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (pp) REVERT: C 620 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8596 (ptp90) REVERT: D 508 GLN cc_start: 0.7437 (tt0) cc_final: 0.7169 (tm-30) REVERT: D 511 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8057 (mt0) REVERT: D 649 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8315 (mp) REVERT: E 413 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: E 454 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8783 (m-30) REVERT: E 643 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6228 (pt) REVERT: F 368 TRP cc_start: 0.8459 (m100) cc_final: 0.7356 (m100) REVERT: F 398 MET cc_start: 0.6929 (mmp) cc_final: 0.6689 (tpt) REVERT: F 416 GLU cc_start: 0.4383 (pm20) cc_final: 0.4092 (tp30) REVERT: F 458 LYS cc_start: 0.4437 (mttt) cc_final: 0.4062 (mtpt) REVERT: F 490 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7015 (mp) outliers start: 29 outliers final: 15 residues processed: 156 average time/residue: 1.1459 time to fit residues: 200.1899 Evaluate side-chains 155 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 497 VAL Chi-restraints excluded: chain A residue 621 SER 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 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 661 LEU Chi-restraints excluded: chain D residue 352 SER 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 504 GLN Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain F residue 490 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 86 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110982 restraints weight = 21822.806| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.02 r_work: 0.3142 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4032 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= 0.140 Angle : 0.564 10.859 21548 Z= 0.286 Chirality : 0.040 0.174 2339 Planarity : 0.004 0.050 2787 Dihedral : 9.122 128.353 2186 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 1.76 % Allowed : 17.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1888 helix: 1.37 (0.17), residues: 917 sheet: -0.14 (0.30), residues: 279 loop : 0.46 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 601 HIS 0.013 0.001 HIS A 505 PHE 0.021 0.001 PHE F 558 TYR 0.028 0.001 TYR A 397 ARG 0.003 0.000 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 728) hydrogen bonds : angle 5.43892 ( 2100) covalent geometry : bond 0.00338 (15994) covalent geometry : angle 0.56369 (21548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13440.14 seconds wall clock time: 237 minutes 12.45 seconds (14232.45 seconds total)