Starting phenix.real_space_refine on Thu Mar 5 04:16:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t8b_10399/03_2026/6t8b_10399.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8b_10399/03_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_10399/03_2026/6t8b_10399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8b_10399/03_2026/6t8b_10399.map" model { file = "/net/cci-nas-00/data/ceres_data/6t8b_10399/03_2026/6t8b_10399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8b_10399/03_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-dev-5986/lib/python3.9/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: 4.87, per 1000 atoms: 0.26 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: 1.46 Conformation dependent library (CDL) restraints added in 883.2 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: 2.30 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: 3.22 Time building geometry restraints manager: 1.96 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=" C VAL F 608 " pdb=" N GLU F 609 " ideal model delta sigma weight residual 1.333 1.307 0.026 1.37e-02 5.33e+03 3.48e+00 bond pdb=" C MET F 459 " pdb=" N PRO F 460 " ideal model delta sigma weight residual 1.338 1.370 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" C MET D 459 " pdb=" N PRO D 460 " ideal model delta sigma weight residual 1.338 1.367 -0.029 1.90e-02 2.77e+03 2.25e+00 bond pdb=" C MET C 459 " pdb=" N PRO C 460 " ideal model delta sigma weight residual 1.338 1.366 -0.028 1.90e-02 2.77e+03 2.18e+00 bond pdb=" C LEU F 463 " pdb=" N VAL F 464 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.29e-02 6.01e+03 1.36e+00 ... (remaining 19487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 26162 2.24 - 4.48: 430 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=" N VAL D 364 " pdb=" CA VAL D 364 " pdb=" C VAL D 364 " ideal model delta sigma weight residual 113.71 110.08 3.63 9.50e-01 1.11e+00 1.46e+01 angle pdb=" C GLU C 596 " pdb=" N PHE C 597 " pdb=" CA PHE C 597 " ideal model delta sigma weight residual 120.28 125.64 -5.36 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C MET A 459 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 120.60 112.99 7.61 2.20e+00 2.07e-01 1.20e+01 ... (remaining 26640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 11721 31.74 - 63.48: 262 63.48 - 95.22: 5 95.22 - 126.95: 4 126.95 - 158.69: 4 Dihedral angle restraints: 11996 sinusoidal: 5186 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 11993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2022 0.036 - 0.072: 781 0.072 - 0.108: 270 0.108 - 0.144: 103 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.340 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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= 0.173 Angle : 0.721 11.199 26645 Z= 0.403 Chirality : 0.046 0.180 3185 Planarity : 0.006 0.066 3236 Dihedral : 12.526 158.693 7580 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 covalent geometry : bond 0.00378 (19492) covalent geometry : angle 0.72141 (26645) hydrogen bonds : bond 0.17852 ( 728) hydrogen bonds : angle 8.27319 ( 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 : 0.713 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: 0.1591 time to fit residues: 146.0685 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 : 0.625 ------------------------------------------------------------------------------- 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: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 383 ASN B 435 HIS B 512 HIS B 617 GLN B 671 GLN C 445 HIS C 645 ASN C 692 HIS C 702 HIS D 383 ASN D 419 GLN D 435 HIS D 477 ASN D 526 ASN D 554 ASN E 445 HIS E 671 GLN F 328 GLN F 383 ASN ** F 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3546 r_free = 0.3546 target = 0.131869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105752 restraints weight = 29096.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107431 restraints weight = 23350.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108398 restraints weight = 16730.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109410 restraints weight = 14413.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109755 restraints weight = 12903.895| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19492 Z= 0.155 Angle : 0.708 8.539 26645 Z= 0.355 Chirality : 0.047 0.290 3185 Planarity : 0.006 0.055 3236 Dihedral : 15.761 173.923 3099 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.15 % Allowed : 10.03 % Favored : 87.82 % 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: -3.14 (0.16), residues: 2346 helix: -1.10 (0.16), residues: 933 sheet: -2.74 (0.23), residues: 390 loop : -2.69 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 548 TYR 0.020 0.002 TYR D 331 PHE 0.014 0.002 PHE C 597 TRP 0.023 0.003 TRP C 530 HIS 0.007 0.001 HIS C 702 Details of bonding type rmsd covalent geometry : bond 0.00356 (19492) covalent geometry : angle 0.70799 (26645) hydrogen bonds : bond 0.04147 ( 728) hydrogen bonds : angle 5.83438 ( 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: 43 poor density : 384 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8103 (ptp-170) cc_final: 0.7846 (mtm-85) REVERT: A 659 ASP cc_start: 0.8051 (m-30) cc_final: 0.7790 (m-30) REVERT: A 665 ASP cc_start: 0.8326 (t0) cc_final: 0.8111 (m-30) REVERT: A 681 LEU cc_start: 0.9296 (tp) cc_final: 0.9054 (tt) REVERT: B 331 TYR cc_start: 0.6980 (m-10) cc_final: 0.5890 (m-10) REVERT: B 446 ASP cc_start: 0.7685 (p0) cc_final: 0.7420 (p0) REVERT: C 715 ASP cc_start: 0.7743 (p0) cc_final: 0.7402 (p0) REVERT: D 716 TYR cc_start: 0.7640 (m-10) cc_final: 0.7273 (m-80) REVERT: E 556 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7633 (mtmm) REVERT: E 600 MET cc_start: 0.7472 (ttp) cc_final: 0.6872 (tpt) REVERT: E 601 MET cc_start: 0.6426 (mmm) cc_final: 0.5907 (tmm) REVERT: E 631 GLN cc_start: 0.7425 (mt0) cc_final: 0.7114 (mm-40) REVERT: E 666 GLN cc_start: 0.8048 (mt0) cc_final: 0.7752 (mt0) REVERT: F 617 GLN cc_start: 0.8479 (mt0) cc_final: 0.8255 (mt0) outliers start: 43 outliers final: 24 residues processed: 414 average time/residue: 0.1399 time to fit residues: 88.7428 Evaluate side-chains 328 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 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 594 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: 0.5980 chunk 116 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 220 optimal weight: 0.0270 chunk 202 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 360 HIS B 383 ASN B 617 GLN C 419 GLN C 617 GLN C 645 ASN D 383 ASN E 477 ASN E 645 ASN E 653 GLN F 328 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 = 0.3551 r_free = 0.3551 target = 0.132354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105488 restraints weight = 29245.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107252 restraints weight = 19103.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108417 restraints weight = 14671.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108822 restraints weight = 12603.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108977 restraints weight = 11748.564| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19492 Z= 0.134 Angle : 0.656 10.053 26645 Z= 0.323 Chirality : 0.046 0.240 3185 Planarity : 0.005 0.047 3236 Dihedral : 15.638 178.148 3099 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.54 % Allowed : 11.98 % 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: -2.51 (0.17), residues: 2346 helix: -0.55 (0.17), residues: 941 sheet: -2.42 (0.24), residues: 384 loop : -2.37 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 529 TYR 0.018 0.002 TYR B 539 PHE 0.014 0.002 PHE C 597 TRP 0.017 0.002 TRP D 530 HIS 0.008 0.001 HIS C 702 Details of bonding type rmsd covalent geometry : bond 0.00310 (19492) covalent geometry : angle 0.65596 (26645) hydrogen bonds : bond 0.03636 ( 728) hydrogen bonds : angle 5.33293 ( 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 394 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 343 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8059 (ptp-170) cc_final: 0.7756 (mtm-85) REVERT: A 659 ASP cc_start: 0.8006 (m-30) cc_final: 0.7366 (m-30) REVERT: B 370 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9168 (pt) REVERT: B 446 ASP cc_start: 0.7618 (p0) cc_final: 0.7398 (p0) REVERT: C 715 ASP cc_start: 0.7714 (p0) cc_final: 0.7410 (p0) REVERT: D 339 MET cc_start: 0.7803 (tpp) cc_final: 0.7294 (tpp) REVERT: D 479 MET cc_start: 0.8591 (mtt) cc_final: 0.8367 (mmt) REVERT: D 678 MET cc_start: 0.7142 (ptt) cc_final: 0.6876 (ptt) REVERT: D 716 TYR cc_start: 0.7642 (m-10) cc_final: 0.7281 (m-80) REVERT: E 317 PRO cc_start: 0.6306 (Cg_endo) cc_final: 0.6034 (Cg_exo) REVERT: E 556 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7619 (mtmm) REVERT: E 601 MET cc_start: 0.6294 (mmm) cc_final: 0.5862 (tmm) REVERT: E 631 GLN cc_start: 0.7327 (mt0) cc_final: 0.7032 (mm-40) outliers start: 51 outliers final: 31 residues processed: 374 average time/residue: 0.1348 time to fit residues: 78.1784 Evaluate side-chains 328 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 663 ILE Chi-restraints excluded: chain B residue 332 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 539 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 539 TYR 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 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 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 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: 2.9990 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 383 ASN B 617 GLN C 419 GLN C 617 GLN D 383 ASN D 477 ASN E 477 ASN F 328 GLN F 360 HIS F 383 ASN F 617 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099788 restraints weight = 29617.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101847 restraints weight = 23418.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102555 restraints weight = 16729.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103092 restraints weight = 14253.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103279 restraints weight = 13165.250| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19492 Z= 0.270 Angle : 0.743 8.364 26645 Z= 0.368 Chirality : 0.049 0.177 3185 Planarity : 0.006 0.047 3236 Dihedral : 15.632 172.486 3099 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.24 % Allowed : 12.92 % Favored : 83.83 % 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: -2.39 (0.17), residues: 2346 helix: -0.47 (0.17), residues: 944 sheet: -2.27 (0.24), residues: 386 loop : -2.33 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 649 TYR 0.017 0.002 TYR A 331 PHE 0.027 0.002 PHE D 423 TRP 0.023 0.003 TRP D 530 HIS 0.010 0.001 HIS F 360 Details of bonding type rmsd covalent geometry : bond 0.00649 (19492) covalent geometry : angle 0.74275 (26645) hydrogen bonds : bond 0.04118 ( 728) hydrogen bonds : angle 5.28993 ( 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 381 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5787 (tptt) REVERT: A 450 ARG cc_start: 0.8243 (ptp-170) cc_final: 0.7866 (mtm-85) REVERT: B 369 GLU cc_start: 0.7879 (tt0) cc_final: 0.7605 (tt0) REVERT: B 370 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9153 (pt) REVERT: B 685 THR cc_start: 0.8967 (m) cc_final: 0.8324 (p) REVERT: C 339 MET cc_start: 0.7481 (ttm) cc_final: 0.7017 (ttm) REVERT: D 339 MET cc_start: 0.7807 (tpp) cc_final: 0.7286 (tpp) REVERT: D 521 MET cc_start: 0.6890 (tpt) cc_final: 0.6585 (tpp) REVERT: D 617 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7235 (tm-30) REVERT: E 427 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8322 (mp) REVERT: E 556 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7622 (mtmm) REVERT: E 601 MET cc_start: 0.6285 (mmm) cc_final: 0.5772 (tmm) REVERT: F 617 GLN cc_start: 0.8520 (mt0) cc_final: 0.8286 (mt0) outliers start: 65 outliers final: 42 residues processed: 362 average time/residue: 0.1217 time to fit residues: 69.5654 Evaluate side-chains 330 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 557 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 332 SER 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 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 696 VAL 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 447 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 502 LEU 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 417 ASP 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 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 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 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 630 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 687 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 192 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 617 GLN C 617 GLN E 477 ASN F 328 GLN F 360 HIS F 383 ASN F 435 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101292 restraints weight = 29192.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103643 restraints weight = 18840.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105228 restraints weight = 14189.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106316 restraints weight = 11725.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107045 restraints weight = 10330.680| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19492 Z= 0.161 Angle : 0.661 8.253 26645 Z= 0.327 Chirality : 0.046 0.183 3185 Planarity : 0.005 0.048 3236 Dihedral : 15.399 177.903 3099 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.09 % Allowed : 13.42 % Favored : 83.48 % 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: -2.05 (0.17), residues: 2346 helix: -0.24 (0.17), residues: 940 sheet: -1.99 (0.26), residues: 377 loop : -2.14 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 418 TYR 0.016 0.001 TYR B 539 PHE 0.015 0.002 PHE D 597 TRP 0.020 0.002 TRP D 530 HIS 0.006 0.001 HIS C 702 Details of bonding type rmsd covalent geometry : bond 0.00381 (19492) covalent geometry : angle 0.66066 (26645) hydrogen bonds : bond 0.03522 ( 728) hydrogen bonds : angle 5.03853 ( 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 359 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 297 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5374 (tptt) REVERT: A 450 ARG cc_start: 0.8197 (ptp-170) cc_final: 0.7811 (mtm-85) REVERT: B 370 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9153 (pt) REVERT: C 653 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8605 (tm-30) REVERT: D 339 MET cc_start: 0.7792 (tpp) cc_final: 0.7314 (tpp) REVERT: D 617 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7558 (tm-30) REVERT: E 427 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (mp) REVERT: E 556 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7522 (ptpp) REVERT: E 601 MET cc_start: 0.6167 (mmm) cc_final: 0.5781 (tmm) outliers start: 62 outliers final: 37 residues processed: 338 average time/residue: 0.1310 time to fit residues: 69.3848 Evaluate side-chains 315 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 419 GLN 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 653 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 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 417 ASP Chi-restraints excluded: chain D residue 501 MET 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 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 539 TYR 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 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: 4.9990 chunk 203 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 HIS B 328 GLN B 617 GLN D 477 ASN E 371 GLN E 477 ASN F 617 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104031 restraints weight = 28941.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106456 restraints weight = 18636.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108083 restraints weight = 13960.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109195 restraints weight = 11503.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109844 restraints weight = 10092.863| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19492 Z= 0.123 Angle : 0.637 13.173 26645 Z= 0.311 Chirality : 0.045 0.177 3185 Planarity : 0.005 0.047 3236 Dihedral : 15.117 173.826 3099 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.54 % Allowed : 14.77 % 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: -1.73 (0.17), residues: 2346 helix: -0.02 (0.18), residues: 948 sheet: -1.80 (0.26), residues: 378 loop : -1.93 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 529 TYR 0.016 0.001 TYR B 539 PHE 0.017 0.002 PHE D 597 TRP 0.017 0.002 TRP D 530 HIS 0.007 0.001 HIS F 360 Details of bonding type rmsd covalent geometry : bond 0.00283 (19492) covalent geometry : angle 0.63653 (26645) hydrogen bonds : bond 0.03166 ( 728) hydrogen bonds : angle 4.79038 ( 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 368 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5142 (tptt) REVERT: A 450 ARG cc_start: 0.8130 (ptp-170) cc_final: 0.7740 (mtm-85) REVERT: B 369 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: C 653 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8590 (tm-30) REVERT: D 339 MET cc_start: 0.7723 (tpp) cc_final: 0.7361 (tpp) REVERT: D 371 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D 459 MET cc_start: 0.7972 (mtt) cc_final: 0.7510 (mtt) REVERT: D 521 MET cc_start: 0.7245 (tpp) cc_final: 0.6376 (tpt) REVERT: D 549 ASN cc_start: 0.7693 (p0) cc_final: 0.7341 (m-40) REVERT: D 617 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7614 (tm-30) REVERT: E 427 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8269 (mp) REVERT: E 556 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7511 (ptpp) REVERT: E 601 MET cc_start: 0.6151 (mmm) cc_final: 0.5768 (tmm) outliers start: 51 outliers final: 32 residues processed: 351 average time/residue: 0.1367 time to fit residues: 74.2316 Evaluate side-chains 321 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 663 ILE Chi-restraints excluded: chain B residue 369 GLU 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 502 LEU Chi-restraints excluded: chain C residue 635 VAL 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 417 ASP Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 685 THR 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 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 655 SER Chi-restraints excluded: chain E residue 663 ILE 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 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: 6.9990 chunk 214 optimal weight: 7.9990 chunk 105 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN B 328 GLN B 617 GLN D 477 ASN F 360 HIS F 617 GLN F 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100968 restraints weight = 29423.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101989 restraints weight = 23936.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103154 restraints weight = 18458.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103709 restraints weight = 15451.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103912 restraints weight = 14551.782| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 19492 Z= 0.237 Angle : 0.716 14.235 26645 Z= 0.351 Chirality : 0.048 0.192 3185 Planarity : 0.005 0.061 3236 Dihedral : 15.101 167.434 3099 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.74 % Allowed : 15.32 % 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: -1.77 (0.17), residues: 2346 helix: -0.07 (0.17), residues: 956 sheet: -1.84 (0.26), residues: 363 loop : -1.94 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 450 TYR 0.014 0.002 TYR B 539 PHE 0.019 0.002 PHE C 597 TRP 0.020 0.002 TRP D 530 HIS 0.008 0.001 HIS F 360 Details of bonding type rmsd covalent geometry : bond 0.00569 (19492) covalent geometry : angle 0.71628 (26645) hydrogen bonds : bond 0.03705 ( 728) hydrogen bonds : angle 4.93378 ( 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 346 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5188 (tptt) REVERT: A 450 ARG cc_start: 0.8241 (ptp-170) cc_final: 0.7852 (mtm-85) REVERT: B 369 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: D 339 MET cc_start: 0.7750 (tpp) cc_final: 0.7290 (tpp) REVERT: D 371 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8544 (tm-30) REVERT: D 459 MET cc_start: 0.7892 (mtt) cc_final: 0.7512 (mtt) REVERT: D 521 MET cc_start: 0.7376 (tpp) cc_final: 0.6856 (tpp) REVERT: D 549 ASN cc_start: 0.7566 (p0) cc_final: 0.7327 (m-40) REVERT: D 617 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7613 (tm-30) REVERT: E 427 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8400 (mp) REVERT: E 477 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7160 (t0) REVERT: E 556 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7567 (ptpp) REVERT: E 601 MET cc_start: 0.6225 (mmm) cc_final: 0.5837 (tmm) REVERT: F 601 MET cc_start: 0.7446 (mmm) cc_final: 0.7226 (mmm) outliers start: 55 outliers final: 43 residues processed: 329 average time/residue: 0.1389 time to fit residues: 70.8448 Evaluate side-chains 322 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 369 GLU 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 B residue 687 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 630 THR 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 360 HIS Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 685 THR 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 600 MET Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 655 SER Chi-restraints excluded: chain E residue 663 ILE 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 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: 0.7980 chunk 120 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 207 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 617 GLN C 617 GLN D 477 ASN E 625 HIS F 360 HIS F 383 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103352 restraints weight = 29013.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105718 restraints weight = 18662.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107316 restraints weight = 13991.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108384 restraints weight = 11560.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109130 restraints weight = 10181.409| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19492 Z= 0.127 Angle : 0.644 12.980 26645 Z= 0.313 Chirality : 0.045 0.171 3185 Planarity : 0.005 0.047 3236 Dihedral : 14.903 155.780 3099 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.40 % Allowed : 16.02 % Favored : 81.59 % 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: -1.56 (0.17), residues: 2346 helix: 0.05 (0.18), residues: 961 sheet: -1.70 (0.27), residues: 362 loop : -1.79 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 529 TYR 0.015 0.001 TYR B 539 PHE 0.015 0.001 PHE C 597 TRP 0.016 0.002 TRP E 530 HIS 0.006 0.001 HIS D 512 Details of bonding type rmsd covalent geometry : bond 0.00298 (19492) covalent geometry : angle 0.64425 (26645) hydrogen bonds : bond 0.03122 ( 728) hydrogen bonds : angle 4.72463 ( 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 340 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5128 (tptt) REVERT: A 450 ARG cc_start: 0.8153 (ptp-170) cc_final: 0.7800 (mtm-85) REVERT: D 339 MET cc_start: 0.7615 (tpp) cc_final: 0.7261 (tpp) REVERT: D 371 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 459 MET cc_start: 0.7964 (mtt) cc_final: 0.7507 (mtt) REVERT: D 521 MET cc_start: 0.7666 (tpp) cc_final: 0.6832 (tpt) REVERT: D 549 ASN cc_start: 0.7623 (p0) cc_final: 0.7325 (m-40) REVERT: D 617 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7598 (tm-30) REVERT: E 427 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8369 (mp) REVERT: E 477 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7229 (t0) REVERT: E 556 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7490 (ptpp) REVERT: E 601 MET cc_start: 0.6363 (mmm) cc_final: 0.5880 (tmm) outliers start: 48 outliers final: 33 residues processed: 327 average time/residue: 0.1329 time to fit residues: 67.6087 Evaluate side-chains 313 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 586 THR 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 502 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 417 ASP Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 685 THR 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 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 600 MET Chi-restraints excluded: chain E residue 663 ILE 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 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: 4.9990 chunk 127 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 162 optimal weight: 0.0870 chunk 117 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN B 328 GLN B 360 HIS ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 702 HIS F 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103269 restraints weight = 29170.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104596 restraints weight = 20449.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105529 restraints weight = 16403.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106313 restraints weight = 13654.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106518 restraints weight = 12387.319| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19492 Z= 0.145 Angle : 0.656 12.047 26645 Z= 0.318 Chirality : 0.045 0.165 3185 Planarity : 0.005 0.062 3236 Dihedral : 14.784 147.882 3099 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.40 % Allowed : 16.07 % Favored : 81.54 % 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: -1.48 (0.18), residues: 2346 helix: 0.09 (0.17), residues: 961 sheet: -1.68 (0.27), residues: 355 loop : -1.71 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 529 TYR 0.014 0.001 TYR B 539 PHE 0.015 0.001 PHE C 597 TRP 0.017 0.002 TRP D 530 HIS 0.006 0.001 HIS F 360 Details of bonding type rmsd covalent geometry : bond 0.00345 (19492) covalent geometry : angle 0.65567 (26645) hydrogen bonds : bond 0.03189 ( 728) hydrogen bonds : angle 4.68865 ( 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 335 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5128 (tptt) REVERT: A 450 ARG cc_start: 0.8179 (ptp-170) cc_final: 0.7811 (mtm-85) REVERT: A 542 MET cc_start: 0.9252 (mtm) cc_final: 0.8476 (mtm) REVERT: C 715 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7084 (p0) REVERT: D 339 MET cc_start: 0.7693 (tpp) cc_final: 0.7315 (tpp) REVERT: D 371 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8507 (tm-30) REVERT: D 521 MET cc_start: 0.7833 (tpp) cc_final: 0.7338 (tpp) REVERT: D 549 ASN cc_start: 0.7621 (p0) cc_final: 0.7397 (m-40) REVERT: D 567 LEU cc_start: 0.7354 (mp) cc_final: 0.7083 (tp) REVERT: D 617 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7631 (tm-30) REVERT: E 427 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8355 (mp) REVERT: E 477 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7196 (t0) REVERT: E 496 MET cc_start: 0.5889 (mtt) cc_final: 0.5627 (mtt) REVERT: E 556 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7519 (ptpp) REVERT: E 601 MET cc_start: 0.6375 (mmm) cc_final: 0.5974 (tmm) REVERT: E 685 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7995 (p) outliers start: 48 outliers final: 36 residues processed: 321 average time/residue: 0.1328 time to fit residues: 67.2292 Evaluate side-chains 315 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 678 MET 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 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 501 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 685 THR 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 467 THR Chi-restraints excluded: chain E residue 477 ASN 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 600 MET Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 685 THR 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 210 optimal weight: 0.0870 chunk 237 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 549 ASN ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105964 restraints weight = 29188.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107005 restraints weight = 24464.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108087 restraints weight = 18090.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108549 restraints weight = 15001.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108956 restraints weight = 13497.844| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19492 Z= 0.125 Angle : 0.645 11.716 26645 Z= 0.314 Chirality : 0.045 0.305 3185 Planarity : 0.005 0.060 3236 Dihedral : 14.624 135.509 3099 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.25 % Allowed : 16.47 % Favored : 81.29 % 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: -1.37 (0.18), residues: 2346 helix: 0.13 (0.18), residues: 961 sheet: -1.58 (0.27), residues: 355 loop : -1.60 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 529 TYR 0.014 0.001 TYR B 539 PHE 0.013 0.001 PHE C 597 TRP 0.016 0.002 TRP E 530 HIS 0.005 0.001 HIS D 512 Details of bonding type rmsd covalent geometry : bond 0.00292 (19492) covalent geometry : angle 0.64512 (26645) hydrogen bonds : bond 0.03057 ( 728) hydrogen bonds : angle 4.61864 ( 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 345 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5717 (OUTLIER) cc_final: 0.4913 (tptt) REVERT: A 450 ARG cc_start: 0.8192 (ptp-170) cc_final: 0.7803 (mtm-85) REVERT: A 542 MET cc_start: 0.9231 (mtm) cc_final: 0.8457 (mtm) REVERT: C 715 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.6994 (p0) REVERT: D 339 MET cc_start: 0.7640 (tpp) cc_final: 0.7291 (tpp) REVERT: D 371 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8499 (tm-30) REVERT: D 521 MET cc_start: 0.7791 (tpp) cc_final: 0.7288 (tpp) REVERT: D 617 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 477 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7288 (t0) REVERT: E 496 MET cc_start: 0.6008 (mtt) cc_final: 0.5796 (mtt) REVERT: E 601 MET cc_start: 0.6170 (mmm) cc_final: 0.5874 (tmm) REVERT: E 685 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7950 (p) outliers start: 45 outliers final: 35 residues processed: 330 average time/residue: 0.1311 time to fit residues: 67.7010 Evaluate side-chains 318 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 678 MET 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 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 501 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN 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 663 ILE Chi-restraints excluded: chain E residue 685 THR 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: 6.9990 chunk 231 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 166 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 HIS F 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105250 restraints weight = 29198.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107684 restraints weight = 18854.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109316 restraints weight = 14093.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110414 restraints weight = 11631.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111053 restraints weight = 10246.450| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19492 Z= 0.123 Angle : 0.656 15.015 26645 Z= 0.316 Chirality : 0.045 0.250 3185 Planarity : 0.005 0.064 3236 Dihedral : 14.522 126.493 3099 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.20 % Allowed : 16.92 % Favored : 80.89 % 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: -1.23 (0.18), residues: 2346 helix: 0.24 (0.18), residues: 952 sheet: -1.51 (0.27), residues: 356 loop : -1.50 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 529 TYR 0.014 0.001 TYR D 716 PHE 0.013 0.001 PHE C 597 TRP 0.015 0.002 TRP E 530 HIS 0.005 0.001 HIS D 512 Details of bonding type rmsd covalent geometry : bond 0.00288 (19492) covalent geometry : angle 0.65551 (26645) hydrogen bonds : bond 0.03029 ( 728) hydrogen bonds : angle 4.57043 ( 2036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2862.38 seconds wall clock time: 50 minutes 32.17 seconds (3032.17 seconds total)