Starting phenix.real_space_refine on Mon May 19 22:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t8b_10399/05_2025/6t8b_10399.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8b_10399/05_2025/6t8b_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_10399/05_2025/6t8b_10399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8b_10399/05_2025/6t8b_10399.map" model { file = "/net/cci-nas-00/data/ceres_data/6t8b_10399/05_2025/6t8b_10399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8b_10399/05_2025/6t8b_10399.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.20, per 1000 atoms: 0.64 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: 4.76 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 5.89 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: 5.69 Time building geometry restraints manager: 5.42 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 46.190 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.004 TRP B 530 HIS 0.004 0.001 HIS B 702 PHE 0.022 0.002 PHE F 423 TYR 0.022 0.002 TYR A 507 ARG 0.007 0.001 ARG E 493 Details of bonding type rmsd hydrogen bonds : bond 0.17852 ( 728) hydrogen bonds : angle 8.27319 ( 2036) covalent geometry : bond 0.00378 (19492) covalent geometry : angle 0.72141 (26645) *********************** 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 : 2.272 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: 0.8580 (mpp) cc_final: 0.8220 (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: 0.7097 (ttp) cc_final: 0.6664 (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: 0.3580 time to fit residues: 327.9655 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 : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 383 ASN B 435 HIS B 512 HIS B 617 GLN B 671 GLN C 645 ASN C 692 HIS C 702 HIS D 383 ASN D 435 HIS D 477 ASN D 526 ASN D 554 ASN E 445 HIS E 645 ASN E 671 GLN F 328 GLN F 383 ASN ** F 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 653 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105158 restraints weight = 29121.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106963 restraints weight = 23508.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107426 restraints weight = 16853.963| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19492 Z= 0.170 Angle : 0.715 8.357 26645 Z= 0.359 Chirality : 0.047 0.289 3185 Planarity : 0.006 0.056 3236 Dihedral : 15.785 173.211 3099 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.10 % Allowed : 10.13 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.16), residues: 2346 helix: -1.14 (0.16), residues: 933 sheet: -2.76 (0.23), residues: 389 loop : -2.72 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 530 HIS 0.011 0.001 HIS C 702 PHE 0.013 0.002 PHE C 597 TYR 0.020 0.002 TYR D 331 ARG 0.007 0.001 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 728) hydrogen bonds : angle 5.88161 ( 2036) covalent geometry : bond 0.00397 (19492) covalent geometry : angle 0.71503 (26645) *********************** 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 418 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 376 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 450 ARG cc_start: 0.8082 (ptp-170) cc_final: 0.7835 (mtm-85) REVERT: A 501 MET cc_start: 0.8603 (mpp) cc_final: 0.8277 (mpp) REVERT: A 665 ASP cc_start: 0.8340 (t0) cc_final: 0.8111 (m-30) REVERT: B 331 TYR cc_start: 0.7107 (m-10) cc_final: 0.6015 (m-10) REVERT: B 446 ASP cc_start: 0.7704 (p0) cc_final: 0.7490 (p0) REVERT: C 715 ASP cc_start: 0.7802 (p0) cc_final: 0.7434 (p0) REVERT: D 716 TYR cc_start: 0.7639 (m-10) cc_final: 0.7340 (m-80) REVERT: E 331 TYR cc_start: 0.6155 (p90) cc_final: 0.5951 (p90) REVERT: E 556 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7634 (mtmm) REVERT: E 600 MET cc_start: 0.7462 (ttp) cc_final: 0.6859 (tpt) REVERT: E 601 MET cc_start: 0.6463 (mmm) cc_final: 0.5923 (tmm) REVERT: E 631 GLN cc_start: 0.7434 (mt0) cc_final: 0.7109 (mm-40) REVERT: E 720 ILE cc_start: 0.7259 (mm) cc_final: 0.7048 (mp) REVERT: F 617 GLN cc_start: 0.8470 (mt0) cc_final: 0.8250 (mt0) outliers start: 42 outliers final: 24 residues processed: 405 average time/residue: 0.3049 time to fit residues: 188.1446 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 : 2.220 ------------------------------------------------------------------------------- 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 191 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 217 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 328 GLN B 360 HIS B 383 ASN B 617 GLN C 419 GLN C 645 ASN D 383 ASN E 477 ASN E 653 GLN F 445 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101365 restraints weight = 29326.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103027 restraints weight = 25098.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104258 restraints weight = 17395.196| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19492 Z= 0.227 Angle : 0.721 10.223 26645 Z= 0.355 Chirality : 0.048 0.203 3185 Planarity : 0.005 0.051 3236 Dihedral : 15.756 177.746 3099 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.04 % Allowed : 11.83 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2346 helix: -0.71 (0.17), residues: 943 sheet: -2.55 (0.24), residues: 382 loop : -2.55 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 530 HIS 0.009 0.001 HIS C 702 PHE 0.016 0.002 PHE A 597 TYR 0.014 0.002 TYR B 539 ARG 0.005 0.001 ARG B 632 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 728) hydrogen bonds : angle 5.47183 ( 2036) covalent geometry : bond 0.00548 (19492) covalent geometry : angle 0.72130 (26645) *********************** 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 381 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.7079 (tptt) cc_final: 0.6865 (tptt) REVERT: A 353 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 450 ARG cc_start: 0.8180 (ptp-170) cc_final: 0.7768 (mtm-85) REVERT: A 501 MET cc_start: 0.8672 (mpp) cc_final: 0.8314 (mpp) REVERT: A 665 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: B 370 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9123 (pt) REVERT: B 446 ASP cc_start: 0.7747 (p0) cc_final: 0.7541 (p0) REVERT: B 685 THR cc_start: 0.8963 (m) cc_final: 0.8380 (p) REVERT: C 339 MET cc_start: 0.7413 (ttm) cc_final: 0.6995 (ttm) REVERT: C 715 ASP cc_start: 0.7860 (p0) cc_final: 0.7566 (p0) REVERT: D 716 TYR cc_start: 0.7426 (m-10) cc_final: 0.7084 (m-10) REVERT: E 317 PRO cc_start: 0.6324 (Cg_endo) cc_final: 0.6056 (Cg_exo) REVERT: E 331 TYR cc_start: 0.5976 (p90) cc_final: 0.5761 (p90) REVERT: E 427 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8318 (mp) REVERT: E 556 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7652 (mtmm) REVERT: E 601 MET cc_start: 0.6405 (mmm) cc_final: 0.5893 (tmm) REVERT: E 720 ILE cc_start: 0.7340 (mm) cc_final: 0.7116 (mp) REVERT: F 401 GLU cc_start: 0.7900 (pt0) cc_final: 0.7669 (mt-10) outliers start: 61 outliers final: 39 residues processed: 357 average time/residue: 0.2914 time to fit residues: 160.2189 Evaluate side-chains 332 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 665 ASP 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 653 GLN Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 515 CYS Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 638 ILE 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 427 LEU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 687 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.017 > 50: distance: 119 - 139: 8.400 distance: 134 - 139: 6.081 distance: 139 - 140: 7.196 distance: 140 - 141: 28.197 distance: 140 - 143: 30.864 distance: 141 - 142: 46.333 distance: 141 - 144: 12.810 distance: 144 - 145: 17.406 distance: 145 - 146: 19.144 distance: 145 - 148: 15.297 distance: 146 - 147: 11.733 distance: 146 - 152: 23.970 distance: 148 - 149: 17.247 distance: 149 - 150: 17.025 distance: 149 - 151: 23.268 distance: 152 - 153: 7.407 distance: 153 - 154: 10.802 distance: 153 - 156: 12.488 distance: 154 - 155: 9.660 distance: 154 - 160: 8.884 distance: 156 - 157: 7.229 distance: 156 - 158: 23.047 distance: 157 - 159: 19.659 distance: 160 - 161: 26.622 distance: 160 - 166: 41.325 distance: 161 - 162: 3.246 distance: 161 - 164: 33.817 distance: 162 - 163: 3.735 distance: 162 - 167: 14.813 distance: 164 - 165: 14.717 distance: 165 - 166: 26.297 distance: 167 - 168: 10.557 distance: 168 - 169: 9.965 distance: 168 - 171: 5.904 distance: 169 - 170: 12.771 distance: 169 - 174: 17.437 distance: 171 - 172: 14.160 distance: 171 - 173: 22.253 distance: 174 - 175: 5.718 distance: 175 - 176: 5.154 distance: 175 - 178: 14.118 distance: 176 - 177: 16.161 distance: 176 - 185: 10.291 distance: 178 - 179: 12.388 distance: 179 - 180: 19.650 distance: 180 - 181: 9.724 distance: 181 - 182: 10.149 distance: 182 - 183: 10.775 distance: 182 - 184: 6.570 distance: 185 - 186: 7.502 distance: 186 - 187: 6.011 distance: 186 - 189: 18.636 distance: 187 - 188: 8.889 distance: 187 - 193: 7.619 distance: 189 - 190: 9.755 distance: 189 - 191: 20.088 distance: 190 - 192: 17.975 distance: 193 - 194: 7.394 distance: 194 - 195: 21.963 distance: 194 - 197: 18.550 distance: 195 - 196: 19.317 distance: 195 - 198: 14.436 distance: 198 - 199: 14.326 distance: 199 - 200: 5.680 distance: 199 - 202: 9.937 distance: 200 - 201: 28.274 distance: 200 - 209: 7.519 distance: 202 - 203: 5.641 distance: 203 - 204: 9.800 distance: 203 - 205: 6.105 distance: 205 - 207: 7.080 distance: 206 - 208: 4.791 distance: 207 - 208: 9.677 distance: 209 - 210: 6.497 distance: 210 - 211: 4.551 distance: 210 - 213: 3.371 distance: 211 - 212: 13.189 distance: 211 - 218: 20.266 distance: 213 - 214: 19.413 distance: 214 - 215: 4.763 distance: 215 - 217: 4.177