Starting phenix.real_space_refine on Sat Sep 12 23:12:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.map" model { file = "/net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t8b_10399/09_2026/6t8b_10399.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 55 5.49 5 Mg 4 5.21 5 S 93 5.16 5 C 11959 2.51 5 N 3294 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19077 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3020 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 368} Chain breaks: 1 Chain: "C" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3021 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 369} Chain breaks: 1 Chain: "D" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2991 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain breaks: 1 Chain: "E" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2991 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain breaks: 1 Chain: "F" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 1 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "H" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.81, per 1000 atoms: 0.25 Number of scatterers: 19077 At special positions: 0 Unit cell: (139.384, 99.56, 135.192, 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 93 16.00 P 55 15.00 Mg 4 11.99 O 3672 8.00 N 3294 7.00 C 11959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 943.6 milliseconds 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 17 sheets defined 40.7% alpha, 12.6% beta 20 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.741A pdb=" N LEU A 321 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.935A pdb=" N PHE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 removed outlier: 4.520A pdb=" N ILE A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.727A pdb=" N LEU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 428' Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.967A pdb=" N ASP A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.733A pdb=" N ASN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 544 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 605 through 619 removed outlier: 4.351A pdb=" N GLU A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.976A pdb=" N ILE A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 710 removed outlier: 3.514A pdb=" N VAL A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.812A pdb=" N LEU B 321 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 423 through 428 Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.509A pdb=" N ASP B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.161A pdb=" N ILE B 506 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 544 Processing helix chain 'B' and resid 549 through 563 removed outlier: 3.576A pdb=" N PHE B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 604 Processing helix chain 'B' and resid 605 through 618 removed outlier: 3.744A pdb=" N GLU B 609 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.916A pdb=" N ILE B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 712 removed outlier: 3.780A pdb=" N LEU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 350 removed outlier: 3.583A pdb=" N MET C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.704A pdb=" N ILE C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 392 removed outlier: 4.211A pdb=" N ARG C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.640A pdb=" N LEU C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 423 through 428' Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.621A pdb=" N ASP C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 520 through 544 Processing helix chain 'C' and resid 549 through 563 Processing helix chain 'C' and resid 596 through 619 removed outlier: 3.925A pdb=" N MET C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS C 606 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS C 607 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU C 610 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU C 611 " --> pdb=" O LYS C 607 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 618 " --> pdb=" O ARG C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 644 Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 697 through 710 removed outlier: 4.107A pdb=" N VAL C 704 " --> pdb=" O GLU C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 721 Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 348 removed outlier: 3.707A pdb=" N GLU D 337 " --> pdb=" O PRO D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 392 removed outlier: 4.095A pdb=" N ILE D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 428 Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 471 through 485 Processing helix chain 'D' and resid 521 through 546 removed outlier: 4.282A pdb=" N ALA D 525 " --> pdb=" O MET D 521 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN D 526 " --> pdb=" O LYS D 522 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 542 " --> pdb=" O ARG D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 563 Processing helix chain 'D' and resid 596 through 601 removed outlier: 4.263A pdb=" N MET D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 616 removed outlier: 3.881A pdb=" N ALA D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 614 " --> pdb=" O GLU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 645 removed outlier: 4.242A pdb=" N ASN D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 664 Processing helix chain 'D' and resid 697 through 710 removed outlier: 3.614A pdb=" N HIS D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 721 removed outlier: 3.625A pdb=" N LEU D 721 " --> pdb=" O GLU D 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 350 removed outlier: 3.538A pdb=" N PHE E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 384 removed outlier: 3.923A pdb=" N ILE E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 392 Processing helix chain 'E' and resid 422 through 428 Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.775A pdb=" N ASP E 433 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 459 No H-bonds generated for 'chain 'E' and resid 457 through 459' Processing helix chain 'E' and resid 471 through 486 removed outlier: 4.021A pdb=" N LYS E 486 " --> pdb=" O SER E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 544 removed outlier: 3.781A pdb=" N ALA E 527 " --> pdb=" O GLU E 523 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG E 540 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 543 " --> pdb=" O TYR E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 560 removed outlier: 3.780A pdb=" N LYS E 556 " --> pdb=" O GLY E 552 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 557 " --> pdb=" O PHE E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 605 removed outlier: 4.166A pdb=" N MET E 600 " --> pdb=" O GLU E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 610 removed outlier: 3.557A pdb=" N GLU E 609 " --> pdb=" O GLY E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 Processing helix chain 'E' and resid 617 through 622 removed outlier: 5.003A pdb=" N ARG E 620 " --> pdb=" O GLN E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 644 removed outlier: 3.621A pdb=" N ALA E 644 " --> pdb=" O GLY E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 664 removed outlier: 3.831A pdb=" N THR E 662 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 712 Processing helix chain 'E' and resid 717 through 721 removed outlier: 3.671A pdb=" N ILE E 720 " --> pdb=" O ILE E 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 Processing helix chain 'F' and resid 325 through 329 removed outlier: 4.052A pdb=" N GLN F 328 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 329 " --> pdb=" O VAL F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 329' Processing helix chain 'F' and resid 332 through 349 Processing helix chain 'F' and resid 378 through 383 Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'F' and resid 422 through 428 removed outlier: 3.615A pdb=" N VAL F 426 " --> pdb=" O ARG F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 520 through 544 removed outlier: 4.084A pdb=" N ALA F 525 " --> pdb=" O MET F 521 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN F 526 " --> pdb=" O LYS F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 563 Processing helix chain 'F' and resid 596 through 605 removed outlier: 3.522A pdb=" N ILE F 603 " --> pdb=" O ASP F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 618 removed outlier: 3.800A pdb=" N ILE F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS F 618 " --> pdb=" O ARG F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 644 Processing helix chain 'F' and resid 658 through 665 removed outlier: 3.979A pdb=" N ILE F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 710 removed outlier: 3.531A pdb=" N VAL F 701 " --> pdb=" O SER F 697 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 707 " --> pdb=" O ARG F 703 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 710 " --> pdb=" O GLU F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 361 removed outlier: 5.480A pdb=" N VAL A 356 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN A 371 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 358 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 398 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 455 removed outlier: 3.542A pdb=" N GLY A 444 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A 454 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA A 442 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 649 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 461 through 462 removed outlier: 6.671A pdb=" N ILE A 495 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 360 removed outlier: 5.416A pdb=" N VAL B 356 " --> pdb=" O GLN B 371 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN B 371 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 398 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 445 removed outlier: 5.364A pdb=" N ALA B 442 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR B 454 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 444 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 492 through 497 removed outlier: 6.984A pdb=" N LEU B 462 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR B 630 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 464 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU B 463 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE B 652 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 465 " --> pdb=" O PHE B 652 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 651 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 361 removed outlier: 7.332A pdb=" N GLU C 369 " --> pdb=" O ASP C 357 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 359 " --> pdb=" O ARG C 367 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG C 367 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 451 through 455 removed outlier: 3.998A pdb=" N GLY C 444 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR C 454 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA C 442 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 495 through 497 removed outlier: 6.308A pdb=" N ILE C 495 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASP C 595 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 497 " --> pdb=" O ASP C 595 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 462 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU C 463 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE C 652 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA C 465 " --> pdb=" O PHE C 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 356 through 361 removed outlier: 3.918A pdb=" N SER D 358 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 451 through 455 removed outlier: 3.697A pdb=" N ILE D 452 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D 651 " --> pdb=" O LEU D 679 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU D 463 " --> pdb=" O ILE D 650 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE D 652 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA D 465 " --> pdb=" O PHE D 652 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 590 " --> pdb=" O HIS D 625 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE D 627 " --> pdb=" O ILE D 590 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL D 592 " --> pdb=" O ILE D 627 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 354 through 360 removed outlier: 7.444A pdb=" N GLU E 369 " --> pdb=" O ASP E 357 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL E 359 " --> pdb=" O ARG E 367 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG E 367 " --> pdb=" O VAL E 359 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 451 through 455 removed outlier: 4.125A pdb=" N GLY E 444 " --> pdb=" O ILE E 452 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR E 454 " --> pdb=" O ALA E 442 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA E 442 " --> pdb=" O THR E 454 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 494 through 497 removed outlier: 3.533A pdb=" N ILE E 495 " --> pdb=" O VAL E 591 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.846A pdb=" N GLU F 369 " --> pdb=" O ASP F 357 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG F 398 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 451 through 455 removed outlier: 7.150A pdb=" N THR F 454 " --> pdb=" O ALA F 442 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA F 442 " --> pdb=" O THR F 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 493 through 497 removed outlier: 6.841A pdb=" N ARG F 493 " --> pdb=" O VAL F 591 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL F 593 " --> pdb=" O ARG F 493 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE F 495 " --> pdb=" O VAL F 593 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6315 1.36 - 1.51: 5241 1.51 - 1.66: 7759 1.66 - 1.80: 153 1.80 - 1.95: 24 Bond restraints: 19492 Sorted by residual: bond pdb=" C3' DA G 17 " pdb=" C2' DA G 17 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DA H 13 " pdb=" C2' DA H 13 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.74e+00 bond pdb=" C3' DA H 11 " pdb=" C2' DA H 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.64e+00 bond pdb=" C3' DT H 20 " pdb=" C2' DT H 20 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.17e+00 bond pdb=" C3' DA G 7 " pdb=" C2' DA G 7 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.16e+00 ... (remaining 19487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 26113 2.24 - 4.48: 479 4.48 - 6.72: 41 6.72 - 8.96: 11 8.96 - 11.20: 1 Bond angle restraints: 26645 Sorted by residual: angle pdb=" N GLN D 617 " pdb=" CA GLN D 617 " pdb=" C GLN D 617 " ideal model delta sigma weight residual 114.75 103.55 11.20 1.26e+00 6.30e-01 7.90e+01 angle pdb=" CA GLN D 617 " pdb=" C GLN D 617 " pdb=" N LYS D 618 " ideal model delta sigma weight residual 119.80 113.48 6.32 1.34e+00 5.57e-01 2.23e+01 angle pdb=" N3 DT H 12 " pdb=" C4 DT H 12 " pdb=" O4 DT H 12 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT G 6 " pdb=" C4 DT G 6 " pdb=" O4 DT G 6 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT G 14 " pdb=" C4 DT G 14 " pdb=" O4 DT G 14 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 26640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 11705 31.74 - 63.48: 245 63.48 - 95.22: 5 95.22 - 126.95: 4 126.95 - 158.69: 4 Dihedral angle restraints: 11963 sinusoidal: 5153 harmonic: 6810 Sorted by residual: dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 98.69 -158.69 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 89.24 -149.24 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 85.64 -145.64 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 11960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1980 0.036 - 0.072: 794 0.072 - 0.108: 290 0.108 - 0.144: 112 0.144 - 0.180: 9 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CA MET F 459 " pdb=" N MET F 459 " pdb=" C MET F 459 " pdb=" CB MET F 459 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ILE F 495 " pdb=" N ILE F 495 " pdb=" C ILE F 495 " pdb=" CB ILE F 495 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA VAL C 474 " pdb=" N VAL C 474 " pdb=" C VAL C 474 " pdb=" CB VAL C 474 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 3182 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 459 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO C 460 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 460 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 460 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 459 " 0.040 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO F 460 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO F 460 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 460 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 459 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 460 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.027 5.00e-02 4.00e+02 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 137 2.53 - 3.12: 15160 3.12 - 3.72: 28892 3.72 - 4.31: 41937 4.31 - 4.90: 68369 Nonbonded interactions: 154495 Sorted by model distance: nonbonded pdb=" O2G AGS B 801 " pdb="MG MG B 802 " model vdw 1.942 2.170 nonbonded pdb=" OG SER B 473 " pdb="MG MG B 802 " model vdw 1.961 2.170 nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 1.965 2.170 nonbonded pdb=" O3B ADP F 801 " pdb="MG MG F 802 " model vdw 1.987 2.170 nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.012 2.170 ... (remaining 154490 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 315 through 570 or resid 586 through 720)) selection = (chain 'B' and (resid 315 through 570 or resid 586 through 720)) selection = (chain 'C' and (resid 315 through 570 or resid 586 through 720)) selection = (chain 'D' and resid 315 through 720) selection = (chain 'E' and resid 315 through 720) selection = (chain 'F' and (resid 315 through 570 or resid 586 through 720)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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 group one per residue 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.020 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.004 0.035 19492 Z= 0.231 Angle : 0.739 11.199 26645 Z= 0.450 Chirality : 0.047 0.180 3185 Planarity : 0.006 0.066 3236 Dihedral : 12.291 158.693 7547 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.14), residues: 2346 helix: -2.26 (0.14), residues: 903 sheet: -3.49 (0.21), residues: 392 loop : -3.22 (0.16), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 493 TYR 0.022 0.002 TYR A 507 PHE 0.022 0.002 PHE F 423 TRP 0.038 0.004 TRP B 530 HIS 0.004 0.001 HIS B 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.23 (19492) covalent geometry : angle 0.73864 / 0.45 (26645) hydrogen bonds : bond 0.17852 / 11.89 ( 728) hydrogen bonds : angle 8.27319 / 5.66 ( 2036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLN cc_start: 0.8684 (tp40) cc_final: 0.8461 (tp40) REVERT: A 450 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7795 (mtm-85) REVERT: A 501 MET cc_start: 0.8579 (mpp) cc_final: 0.8219 (mpp) REVERT: A 681 LEU cc_start: 0.9283 (tp) cc_final: 0.9072 (tt) REVERT: B 446 ASP cc_start: 0.7638 (p0) cc_final: 0.7396 (p0) REVERT: B 517 VAL cc_start: 0.9322 (t) cc_final: 0.9057 (t) REVERT: B 549 ASN cc_start: 0.9111 (p0) cc_final: 0.8825 (p0) REVERT: B 590 ILE cc_start: 0.9326 (mm) cc_final: 0.9079 (mt) REVERT: C 327 LYS cc_start: 0.7630 (pmmt) cc_final: 0.6611 (pmmt) REVERT: C 339 MET cc_start: 0.7627 (ttm) cc_final: 0.7066 (ttm) REVERT: C 455 ASP cc_start: 0.8400 (t0) cc_final: 0.8196 (t0) REVERT: C 506 ILE cc_start: 0.9440 (tp) cc_final: 0.8917 (tp) REVERT: C 631 GLN cc_start: 0.7755 (mt0) cc_final: 0.7495 (mt0) REVERT: D 331 TYR cc_start: 0.6242 (m-10) cc_final: 0.5825 (m-80) REVERT: D 443 LEU cc_start: 0.7605 (mt) cc_final: 0.7344 (mt) REVERT: D 489 PRO cc_start: 0.6375 (Cg_exo) cc_final: 0.5939 (Cg_endo) REVERT: D 607 LYS cc_start: 0.7752 (mttm) cc_final: 0.7470 (mppt) REVERT: D 675 HIS cc_start: 0.8525 (m-70) cc_final: 0.8207 (m-70) REVERT: D 716 TYR cc_start: 0.7850 (m-10) cc_final: 0.7279 (m-80) REVERT: E 500 LYS cc_start: 0.7906 (mttm) cc_final: 0.7417 (mttm) REVERT: E 529 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7267 (ptt90) REVERT: E 556 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7654 (mtmt) REVERT: E 599 ASP cc_start: 0.6345 (m-30) cc_final: 0.6086 (m-30) REVERT: E 600 MET cc_start: 0.7096 (ttp) cc_final: 0.6663 (tpt) REVERT: E 601 MET cc_start: 0.6313 (mmm) cc_final: 0.5682 (tmm) REVERT: E 666 GLN cc_start: 0.7714 (mt0) cc_final: 0.7020 (mt0) REVERT: E 695 PHE cc_start: 0.8144 (t80) cc_final: 0.7807 (t80) REVERT: F 345 ILE cc_start: 0.8939 (mm) cc_final: 0.8654 (mt) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.1715 time to fit residues: 158.5532 Evaluate side-chains 364 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 HIS B 328 GLN B 383 ASN B 435 HIS B 512 HIS B 617 GLN B 671 GLN C 645 ASN C 692 HIS C 702 HIS D 383 ASN D 435 HIS D 477 ASN D 526 ASN D 554 ASN E 445 HIS E 645 ASN E 671 GLN F 328 GLN F 383 ASN F 512 HIS F 617 GLN F 653 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105898 restraints weight = 29128.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107883 restraints weight = 23903.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108385 restraints weight = 16595.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109030 restraints weight = 14411.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109342 restraints weight = 12805.655| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19492 Z= 0.161 Angle : 0.724 8.694 26645 Z= 0.367 Chirality : 0.048 0.248 3185 Planarity : 0.006 0.054 3236 Dihedral : 15.513 171.329 3066 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.20 % Allowed : 9.88 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.16), residues: 2346 helix: -1.21 (0.16), residues: 928 sheet: -2.78 (0.23), residues: 389 loop : -2.73 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 548 TYR 0.019 0.002 TYR D 331 PHE 0.013 0.002 PHE A 597 TRP 0.023 0.003 TRP C 530 HIS 0.005 0.001 HIS C 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (19492) covalent geometry : angle 0.72424 / 0.37 (26645) hydrogen bonds : bond 0.04667 / 3.17 ( 728) hydrogen bonds : angle 6.01516 / 4.09 ( 2036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 383 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 450 ARG cc_start: 0.8079 (ptp-170) cc_final: 0.7842 (mtm-85) REVERT: A 501 MET cc_start: 0.8582 (mpp) cc_final: 0.8237 (mpp) REVERT: A 665 ASP cc_start: 0.8340 (t0) cc_final: 0.8102 (m-30) REVERT: B 331 TYR cc_start: 0.7009 (m-10) cc_final: 0.5927 (m-10) REVERT: B 446 ASP cc_start: 0.7699 (p0) cc_final: 0.7466 (p0) REVERT: C 455 ASP cc_start: 0.8391 (t0) cc_final: 0.8150 (t0) REVERT: D 716 TYR cc_start: 0.7663 (m-10) cc_final: 0.7292 (m-80) REVERT: E 400 VAL cc_start: 0.9461 (t) cc_final: 0.9258 (p) REVERT: E 556 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7618 (mtmm) REVERT: E 600 MET cc_start: 0.7497 (ttp) cc_final: 0.7004 (tpt) REVERT: E 601 MET cc_start: 0.6449 (mmm) cc_final: 0.5940 (tmm) REVERT: E 720 ILE cc_start: 0.7247 (mm) cc_final: 0.7027 (mp) outliers start: 44 outliers final: 26 residues processed: 411 average time/residue: 0.1403 time to fit residues: 89.1150 Evaluate side-chains 333 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN B 328 GLN B 360 HIS B 383 ASN B 617 GLN C 419 GLN C 445 HIS C 645 ASN D 383 ASN E 477 ASN E 653 GLN F 445 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103689 restraints weight = 29308.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105175 restraints weight = 20378.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106015 restraints weight = 16293.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107258 restraints weight = 13126.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107340 restraints weight = 11815.538| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19492 Z= 0.166 Angle : 0.690 10.624 26645 Z= 0.343 Chirality : 0.047 0.203 3185 Planarity : 0.005 0.051 3236 Dihedral : 15.537 178.514 3066 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.89 % Allowed : 11.63 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.16), residues: 2346 helix: -0.74 (0.17), residues: 943 sheet: -2.58 (0.23), residues: 382 loop : -2.47 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 632 TYR 0.016 0.002 TYR B 539 PHE 0.013 0.002 PHE C 652 TRP 0.019 0.003 TRP D 530 HIS 0.005 0.001 HIS C 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (19492) covalent geometry : angle 0.69028 / 0.34 (26645) hydrogen bonds : bond 0.04105 / 2.79 ( 728) hydrogen bonds : angle 5.53518 / 3.78 ( 2036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 329 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 450 ARG cc_start: 0.8096 (ptp-170) cc_final: 0.7726 (mtm-85) REVERT: A 665 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: B 370 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9090 (pt) REVERT: B 446 ASP cc_start: 0.7700 (p0) cc_final: 0.7487 (p0) REVERT: B 517 VAL cc_start: 0.9472 (t) cc_final: 0.9269 (t) REVERT: B 549 ASN cc_start: 0.9094 (p0) cc_final: 0.8866 (p0) REVERT: B 685 THR cc_start: 0.8925 (m) cc_final: 0.8324 (p) REVERT: D 371 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8440 (tm-30) REVERT: D 716 TYR cc_start: 0.7667 (m-10) cc_final: 0.7286 (m-80) REVERT: E 317 PRO cc_start: 0.6286 (Cg_endo) cc_final: 0.6000 (Cg_exo) REVERT: E 556 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7598 (mtmm) REVERT: E 600 MET cc_start: 0.7491 (ttp) cc_final: 0.6822 (tpt) REVERT: E 601 MET cc_start: 0.6341 (mmm) cc_final: 0.5881 (tmm) REVERT: E 720 ILE cc_start: 0.7271 (mm) cc_final: 0.7038 (mp) outliers start: 58 outliers final: 35 residues processed: 363 average time/residue: 0.1394 time to fit residues: 78.6523 Evaluate side-chains 328 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 57 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 360 HIS B 383 ASN B 617 GLN C 419 GLN C 645 ASN D 383 ASN D 477 ASN E 477 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100853 restraints weight = 29512.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102089 restraints weight = 21655.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102897 restraints weight = 16339.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103312 restraints weight = 14584.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103621 restraints weight = 13209.802| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19492 Z= 0.242 Angle : 0.724 8.579 26645 Z= 0.358 Chirality : 0.048 0.186 3185 Planarity : 0.005 0.048 3236 Dihedral : 15.497 176.537 3066 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.29 % Allowed : 12.43 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.17), residues: 2346 helix: -0.59 (0.17), residues: 946 sheet: -2.40 (0.24), residues: 382 loop : -2.41 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 529 TYR 0.018 0.002 TYR B 539 PHE 0.018 0.002 PHE C 597 TRP 0.020 0.003 TRP D 530 HIS 0.006 0.001 HIS B 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (19492) covalent geometry : angle 0.72360 / 0.36 (26645) hydrogen bonds : bond 0.04112 / 2.79 ( 728) hydrogen bonds : angle 5.39858 / 3.69 ( 2036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.5945 (tptt) REVERT: A 353 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 450 ARG cc_start: 0.8163 (ptp-170) cc_final: 0.7821 (mtm-85) REVERT: A 665 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: B 370 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9113 (pt) REVERT: C 715 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7460 (p0) REVERT: D 339 MET cc_start: 0.7639 (tpp) cc_final: 0.7253 (tpp) REVERT: D 371 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8456 (tm-30) REVERT: D 521 MET cc_start: 0.7004 (tpt) cc_final: 0.6651 (tpp) REVERT: D 545 MET cc_start: 0.5884 (tmm) cc_final: 0.5390 (tpp) REVERT: D 716 TYR cc_start: 0.7449 (m-10) cc_final: 0.7059 (m-10) REVERT: E 427 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8271 (mp) REVERT: E 556 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7608 (mtmm) REVERT: E 601 MET cc_start: 0.6270 (mmm) cc_final: 0.5844 (tmm) REVERT: E 720 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7053 (mp) outliers start: 66 outliers final: 43 residues processed: 339 average time/residue: 0.1393 time to fit residues: 73.9335 Evaluate side-chains 331 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 282 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 192 optimal weight: 0.4980 chunk 86 optimal weight: 0.0050 chunk 196 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN A 702 HIS B 328 GLN B 383 ASN B 617 GLN C 645 ASN D 419 GLN E 477 ASN F 328 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103997 restraints weight = 29014.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105771 restraints weight = 19062.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106644 restraints weight = 14567.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107117 restraints weight = 12644.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107494 restraints weight = 12008.049| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19492 Z= 0.129 Angle : 0.659 7.545 26645 Z= 0.327 Chirality : 0.046 0.185 3185 Planarity : 0.005 0.053 3236 Dihedral : 15.321 177.907 3066 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.04 % Allowed : 12.67 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.17), residues: 2346 helix: -0.31 (0.17), residues: 934 sheet: -2.12 (0.25), residues: 380 loop : -2.16 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 418 TYR 0.017 0.001 TYR B 539 PHE 0.016 0.001 PHE A 597 TRP 0.018 0.002 TRP D 530 HIS 0.003 0.001 HIS D 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (19492) covalent geometry : angle 0.65949 / 0.33 (26645) hydrogen bonds : bond 0.03556 / 2.43 ( 728) hydrogen bonds : angle 5.12651 / 3.50 ( 2036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5806 (tptt) REVERT: A 353 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 450 ARG cc_start: 0.8113 (ptp-170) cc_final: 0.7753 (mtm-85) REVERT: B 370 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9137 (pt) REVERT: C 653 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8509 (tm-30) REVERT: D 339 MET cc_start: 0.7567 (tpp) cc_final: 0.7202 (tpp) REVERT: D 371 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 521 MET cc_start: 0.7155 (tpt) cc_final: 0.6866 (tpp) REVERT: D 617 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7517 (tm-30) REVERT: D 653 GLN cc_start: 0.8567 (pt0) cc_final: 0.8335 (tt0) REVERT: D 716 TYR cc_start: 0.7623 (m-10) cc_final: 0.7231 (m-10) REVERT: E 427 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8179 (mp) REVERT: E 556 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7581 (mtmm) REVERT: E 601 MET cc_start: 0.6196 (mmm) cc_final: 0.5780 (tmm) REVERT: E 612 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7389 (mp) REVERT: F 630 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8358 (p) outliers start: 61 outliers final: 38 residues processed: 371 average time/residue: 0.1294 time to fit residues: 75.7083 Evaluate side-chains 333 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 69 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 328 GLN B 383 ASN B 617 GLN C 419 GLN C 617 GLN D 477 ASN E 371 GLN E 477 ASN F 360 HIS F 383 ASN F 435 HIS F 617 GLN F 645 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102994 restraints weight = 29078.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104923 restraints weight = 19774.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105636 restraints weight = 15180.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106177 restraints weight = 13083.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106343 restraints weight = 12225.836| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19492 Z= 0.147 Angle : 0.660 13.153 26645 Z= 0.327 Chirality : 0.046 0.177 3185 Planarity : 0.005 0.047 3236 Dihedral : 15.235 178.180 3066 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.04 % Allowed : 13.57 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.17), residues: 2346 helix: -0.18 (0.17), residues: 945 sheet: -2.00 (0.25), residues: 380 loop : -2.01 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 529 TYR 0.015 0.001 TYR B 539 PHE 0.030 0.002 PHE A 597 TRP 0.018 0.002 TRP D 530 HIS 0.009 0.001 HIS F 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (19492) covalent geometry : angle 0.66012 / 0.33 (26645) hydrogen bonds : bond 0.03538 / 2.40 ( 728) hydrogen bonds : angle 5.00039 / 3.42 ( 2036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5646 (tptt) REVERT: A 353 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 450 ARG cc_start: 0.8157 (ptp-170) cc_final: 0.7760 (mtm-85) REVERT: A 597 PHE cc_start: 0.8731 (t80) cc_final: 0.8305 (t80) REVERT: B 600 MET cc_start: 0.8526 (ttp) cc_final: 0.7814 (ttt) REVERT: C 599 ASP cc_start: 0.7813 (m-30) cc_final: 0.7537 (m-30) REVERT: D 339 MET cc_start: 0.7530 (tpp) cc_final: 0.7193 (tpp) REVERT: D 371 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8413 (tm-30) REVERT: D 617 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7574 (tm-30) REVERT: D 653 GLN cc_start: 0.8574 (pt0) cc_final: 0.8350 (tt0) REVERT: E 427 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8213 (mp) REVERT: E 556 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7629 (mtmm) REVERT: E 601 MET cc_start: 0.6109 (mmm) cc_final: 0.5675 (tmm) REVERT: E 612 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7326 (mp) REVERT: F 617 GLN cc_start: 0.8424 (mt0) cc_final: 0.8179 (mt0) REVERT: F 630 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8399 (p) outliers start: 61 outliers final: 40 residues processed: 347 average time/residue: 0.1362 time to fit residues: 73.5045 Evaluate side-chains 325 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 80 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 328 GLN B 383 ASN B 617 GLN F 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102267 restraints weight = 29317.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104327 restraints weight = 19694.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104948 restraints weight = 14989.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105475 restraints weight = 13179.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105745 restraints weight = 12352.685| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19492 Z= 0.169 Angle : 0.671 10.849 26645 Z= 0.330 Chirality : 0.046 0.173 3185 Planarity : 0.005 0.046 3236 Dihedral : 15.170 175.941 3066 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.24 % Allowed : 14.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.17), residues: 2346 helix: -0.10 (0.17), residues: 949 sheet: -1.96 (0.25), residues: 374 loop : -1.97 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 661 TYR 0.015 0.001 TYR B 539 PHE 0.017 0.002 PHE C 597 TRP 0.018 0.002 TRP D 530 HIS 0.003 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (19492) covalent geometry : angle 0.67056 / 0.33 (26645) hydrogen bonds : bond 0.03559 / 2.43 ( 728) hydrogen bonds : angle 4.91730 / 3.37 ( 2036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 295 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5498 (tptt) REVERT: A 353 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 450 ARG cc_start: 0.8190 (ptp-170) cc_final: 0.7778 (mtm-85) REVERT: C 645 ASN cc_start: 0.8524 (m110) cc_final: 0.8315 (m110) REVERT: D 339 MET cc_start: 0.7608 (tpp) cc_final: 0.7281 (tpp) REVERT: D 371 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8441 (tm-30) REVERT: D 459 MET cc_start: 0.7954 (mtt) cc_final: 0.7560 (mtt) REVERT: D 521 MET cc_start: 0.7034 (tpp) cc_final: 0.6168 (tpt) REVERT: D 549 ASN cc_start: 0.7816 (p0) cc_final: 0.7312 (m-40) REVERT: D 617 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 690 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7898 (ttt180) REVERT: E 427 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8255 (mp) REVERT: E 477 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7432 (t0) REVERT: E 556 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7528 (ptpp) REVERT: E 601 MET cc_start: 0.6118 (mmm) cc_final: 0.5710 (tmm) REVERT: E 612 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7460 (mp) REVERT: F 630 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (p) outliers start: 65 outliers final: 46 residues processed: 341 average time/residue: 0.1405 time to fit residues: 74.9611 Evaluate side-chains 332 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 281 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 600 MET Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 0.0000 chunk 78 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 383 ASN B 617 GLN C 617 GLN D 477 ASN E 625 HIS E 702 HIS F 360 HIS F 383 ASN F 617 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102775 restraints weight = 29243.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105153 restraints weight = 18981.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106753 restraints weight = 14304.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107767 restraints weight = 11832.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108525 restraints weight = 10480.255| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19492 Z= 0.134 Angle : 0.653 10.368 26645 Z= 0.321 Chirality : 0.045 0.173 3185 Planarity : 0.005 0.049 3236 Dihedral : 15.114 174.296 3066 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.89 % Allowed : 14.62 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2346 helix: -0.01 (0.17), residues: 950 sheet: -1.94 (0.26), residues: 367 loop : -1.85 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 661 TYR 0.015 0.001 TYR B 539 PHE 0.016 0.001 PHE C 597 TRP 0.017 0.002 TRP D 530 HIS 0.008 0.001 HIS F 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (19492) covalent geometry : angle 0.65264 / 0.32 (26645) hydrogen bonds : bond 0.03366 / 2.31 ( 728) hydrogen bonds : angle 4.82576 / 3.31 ( 2036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 295 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5230 (tptt) REVERT: A 450 ARG cc_start: 0.8112 (ptp-170) cc_final: 0.7750 (mtm-85) REVERT: B 398 ARG cc_start: 0.7774 (ptm-80) cc_final: 0.7238 (ttp-110) REVERT: D 339 MET cc_start: 0.7548 (tpp) cc_final: 0.7227 (tpp) REVERT: D 371 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 459 MET cc_start: 0.7984 (mtt) cc_final: 0.7574 (mtt) REVERT: D 521 MET cc_start: 0.7075 (tpp) cc_final: 0.6515 (tpp) REVERT: D 617 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7583 (tm-30) REVERT: D 653 GLN cc_start: 0.8569 (pt0) cc_final: 0.8355 (tt0) REVERT: E 427 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8246 (mp) REVERT: E 477 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7450 (t0) REVERT: E 556 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7511 (ptpp) REVERT: E 601 MET cc_start: 0.6215 (mmm) cc_final: 0.5716 (tmm) REVERT: E 612 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7490 (mp) REVERT: E 666 GLN cc_start: 0.7586 (mt0) cc_final: 0.7277 (mt0) REVERT: F 630 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8337 (p) outliers start: 58 outliers final: 44 residues processed: 334 average time/residue: 0.1367 time to fit residues: 71.2640 Evaluate side-chains 326 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain E residue 349 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 163 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 617 GLN D 477 ASN F 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103653 restraints weight = 29244.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104387 restraints weight = 22375.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105259 restraints weight = 18161.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106378 restraints weight = 15188.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106386 restraints weight = 13145.650| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19492 Z= 0.153 Angle : 0.663 10.896 26645 Z= 0.326 Chirality : 0.046 0.210 3185 Planarity : 0.005 0.065 3236 Dihedral : 15.009 177.851 3066 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.84 % Allowed : 15.22 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2346 helix: 0.04 (0.17), residues: 950 sheet: -1.86 (0.26), residues: 354 loop : -1.78 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 529 TYR 0.014 0.001 TYR B 539 PHE 0.015 0.002 PHE C 597 TRP 0.018 0.002 TRP D 530 HIS 0.004 0.001 HIS E 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (19492) covalent geometry : angle 0.66330 / 0.33 (26645) hydrogen bonds : bond 0.03424 / 2.34 ( 728) hydrogen bonds : angle 4.79218 / 3.28 ( 2036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5181 (tptt) REVERT: A 450 ARG cc_start: 0.8177 (ptp-170) cc_final: 0.7818 (mtm-85) REVERT: A 542 MET cc_start: 0.9221 (mtm) cc_final: 0.8529 (mtm) REVERT: D 339 MET cc_start: 0.7610 (tpp) cc_final: 0.7291 (tpp) REVERT: D 371 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8418 (tm-30) REVERT: D 459 MET cc_start: 0.7817 (mtt) cc_final: 0.7424 (mtt) REVERT: D 521 MET cc_start: 0.7555 (tpp) cc_final: 0.6779 (tpt) REVERT: D 549 ASN cc_start: 0.7680 (p0) cc_final: 0.7362 (m-40) REVERT: D 617 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7620 (tm-30) REVERT: D 653 GLN cc_start: 0.8575 (pt0) cc_final: 0.8375 (tt0) REVERT: E 427 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 477 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7449 (t0) REVERT: E 556 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7540 (ptpp) REVERT: E 601 MET cc_start: 0.6266 (mmm) cc_final: 0.5848 (tmm) REVERT: E 612 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7508 (mp) REVERT: E 666 GLN cc_start: 0.7568 (mt0) cc_final: 0.7275 (mt0) REVERT: F 601 MET cc_start: 0.7328 (mmm) cc_final: 0.7115 (mmm) REVERT: F 630 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8364 (p) outliers start: 57 outliers final: 44 residues processed: 326 average time/residue: 0.1387 time to fit residues: 70.5012 Evaluate side-chains 322 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain E residue 349 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 600 MET Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 210 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 617 GLN C 435 HIS ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN F 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105334 restraints weight = 29011.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106269 restraints weight = 24258.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107714 restraints weight = 18279.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108248 restraints weight = 15241.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108527 restraints weight = 14006.821| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19492 Z= 0.133 Angle : 0.655 10.013 26645 Z= 0.322 Chirality : 0.046 0.214 3185 Planarity : 0.005 0.061 3236 Dihedral : 14.904 173.532 3066 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.59 % Allowed : 15.37 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2346 helix: 0.12 (0.18), residues: 952 sheet: -1.79 (0.26), residues: 366 loop : -1.69 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 529 TYR 0.015 0.001 TYR B 539 PHE 0.013 0.001 PHE C 597 TRP 0.017 0.002 TRP D 530 HIS 0.003 0.001 HIS F 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (19492) covalent geometry : angle 0.65458 / 0.32 (26645) hydrogen bonds : bond 0.03243 / 2.22 ( 728) hydrogen bonds : angle 4.71828 / 3.23 ( 2036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5090 (tptt) REVERT: A 450 ARG cc_start: 0.8172 (ptp-170) cc_final: 0.7808 (mtm-85) REVERT: A 542 MET cc_start: 0.9231 (mtm) cc_final: 0.8478 (mtm) REVERT: D 339 MET cc_start: 0.7598 (tpp) cc_final: 0.7283 (tpp) REVERT: D 371 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 521 MET cc_start: 0.7528 (tpp) cc_final: 0.6728 (tpt) REVERT: D 549 ASN cc_start: 0.7530 (p0) cc_final: 0.7301 (m-40) REVERT: D 617 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7586 (tm-30) REVERT: E 427 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8343 (mp) REVERT: E 477 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7343 (t0) REVERT: E 556 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7566 (ptpp) REVERT: E 601 MET cc_start: 0.6249 (mmm) cc_final: 0.5927 (tmm) REVERT: E 612 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7498 (mp) REVERT: E 666 GLN cc_start: 0.7518 (mt0) cc_final: 0.7039 (mt0) outliers start: 52 outliers final: 40 residues processed: 326 average time/residue: 0.1385 time to fit residues: 69.7473 Evaluate side-chains 319 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 275 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 196 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 231 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 328 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103587 restraints weight = 29199.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105242 restraints weight = 20497.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106288 restraints weight = 15581.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107018 restraints weight = 13500.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107177 restraints weight = 12540.934| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19492 Z= 0.145 Angle : 0.664 10.990 26645 Z= 0.325 Chirality : 0.046 0.209 3185 Planarity : 0.005 0.060 3236 Dihedral : 14.839 167.902 3066 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.54 % Allowed : 15.47 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.17), residues: 2346 helix: 0.12 (0.17), residues: 956 sheet: -1.70 (0.27), residues: 354 loop : -1.69 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 529 TYR 0.014 0.001 TYR B 539 PHE 0.014 0.001 PHE C 597 TRP 0.017 0.002 TRP D 530 HIS 0.009 0.001 HIS F 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (19492) covalent geometry : angle 0.66446 / 0.33 (26645) hydrogen bonds : bond 0.03281 / 2.23 ( 728) hydrogen bonds : angle 4.71124 / 3.23 ( 2036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.50 seconds wall clock time: 53 minutes 22.18 seconds (3202.18 seconds total)