Starting phenix.real_space_refine on Sat Sep 12 22:40:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.map" model { file = "/net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8g_10400/09_2026/6t8g_10400.cif" } resolution = 4.34 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= 0.003 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: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 90 5.16 5 C 11870 2.51 5 N 3262 2.21 5 O 3609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18875 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': 27, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2976 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3013 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 368} 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: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 368} Chain breaks: 1 Chain: "F" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3021 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 368} Chain breaks: 1 Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.25 Number of scatterers: 18875 At special positions: 0 Unit cell: (139.384, 104.8, 135.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 44 15.00 O 3609 8.00 N 3262 7.00 C 11870 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: 1.49 Conformation dependent library (CDL) restraints added in 783.8 milliseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 20 sheets defined 40.7% alpha, 12.8% beta 16 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 317 through 321 removed outlier: 4.486A pdb=" N LEU A 320 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 321 " --> pdb=" O LEU A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 321' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.849A pdb=" N MET A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.595A pdb=" N VAL A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 4.021A pdb=" N ASP A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.579A pdb=" N PHE A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.575A pdb=" N ILE A 506 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 507 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 546 removed outlier: 4.835A pdb=" N ASN A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.820A pdb=" N LYS A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 removed outlier: 4.006A pdb=" N MET A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 617 removed outlier: 3.566A pdb=" N ALA A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 removed outlier: 3.898A pdb=" N ALA A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 668 through 672 removed outlier: 3.781A pdb=" N LEU A 672 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 711 Processing helix chain 'B' and resid 328 through 332 removed outlier: 4.282A pdb=" N TYR B 331 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 332 " --> pdb=" O LYS B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 335 through 350 removed outlier: 3.697A pdb=" N MET B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 521 through 545 removed outlier: 3.609A pdb=" N ARG B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 543 " --> pdb=" O TYR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 562 Processing helix chain 'B' and resid 597 through 604 Processing helix chain 'B' and resid 606 through 613 Processing helix chain 'B' and resid 619 through 623 removed outlier: 4.109A pdb=" N GLY B 623 " --> pdb=" O ARG B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 658 through 663 removed outlier: 4.462A pdb=" N ILE B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 711 removed outlier: 3.763A pdb=" N ARG B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 349 removed outlier: 3.526A pdb=" N LEU C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 384 through 390 Processing helix chain 'C' and resid 422 through 428 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 475 through 485 Processing helix chain 'C' and resid 520 through 544 removed outlier: 4.183A pdb=" N ASN C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 596 through 604 removed outlier: 3.580A pdb=" N MET C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 619 Processing helix chain 'C' and resid 656 through 664 removed outlier: 3.513A pdb=" N LEU C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 709 removed outlier: 4.250A pdb=" N GLU C 706 " --> pdb=" O HIS C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 712 No H-bonds generated for 'chain 'C' and resid 710 through 712' Processing helix chain 'C' and resid 717 through 721 removed outlier: 3.649A pdb=" N LEU C 721 " --> pdb=" O GLU C 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.590A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 321 " --> pdb=" O LEU D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 321' Processing helix chain 'D' and resid 332 through 350 Processing helix chain 'D' and resid 378 through 383 Processing helix chain 'D' and resid 384 through 393 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 471 through 485 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.615A pdb=" N ILE D 506 " --> pdb=" O GLU D 503 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR D 507 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 546 Processing helix chain 'D' and resid 549 through 564 removed outlier: 3.546A pdb=" N PHE D 553 " --> pdb=" O ASN D 549 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 563 " --> pdb=" O ASP D 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 604 removed outlier: 4.107A pdb=" N MET D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 604 " --> pdb=" O MET D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 618 removed outlier: 4.090A pdb=" N GLU D 609 " --> pdb=" O GLY D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 646 removed outlier: 4.498A pdb=" N ASN D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 646 " --> pdb=" O ILE D 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 641 through 646' Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'D' and resid 668 through 672 removed outlier: 4.215A pdb=" N LEU D 672 " --> pdb=" O ALA D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 712 removed outlier: 3.787A pdb=" N VAL D 701 " --> pdb=" O SER D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 721 removed outlier: 3.912A pdb=" N ILE D 720 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU D 721 " --> pdb=" O GLU D 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 717 through 721' Processing helix chain 'E' and resid 317 through 321 removed outlier: 4.138A pdb=" N LEU E 320 " --> pdb=" O PRO E 317 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 321 " --> pdb=" O LEU E 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 317 through 321' Processing helix chain 'E' and resid 332 through 349 Processing helix chain 'E' and resid 378 through 383 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 434 removed outlier: 3.715A pdb=" N ASP E 433 " --> pdb=" O SER E 429 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 434 " --> pdb=" O PRO E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 434' Processing helix chain 'E' and resid 471 through 484 Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.827A pdb=" N ILE E 506 " --> pdb=" O GLU E 503 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 508 " --> pdb=" O SER E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 546 removed outlier: 3.520A pdb=" N ASN E 526 " --> pdb=" O LYS E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 564 removed outlier: 3.943A pdb=" N ALA E 563 " --> pdb=" O ASP E 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY E 564 " --> pdb=" O ALA E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 603 Processing helix chain 'E' and resid 605 through 618 removed outlier: 4.322A pdb=" N GLU E 609 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 618 " --> pdb=" O ARG E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 664 Processing helix chain 'E' and resid 697 through 711 removed outlier: 3.625A pdb=" N VAL E 701 " --> pdb=" O SER E 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 711 " --> pdb=" O ALA E 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 removed outlier: 3.630A pdb=" N LEU F 320 " --> pdb=" O PRO F 317 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 321 " --> pdb=" O LEU F 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 317 through 321' Processing helix chain 'F' and resid 332 through 349 Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'F' and resid 384 through 392 Processing helix chain 'F' and resid 423 through 428 Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.895A pdb=" N ASP F 433 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 521 through 546 Processing helix chain 'F' and resid 549 through 563 removed outlier: 3.565A pdb=" N PHE F 553 " --> pdb=" O ASN F 549 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 603 removed outlier: 3.776A pdb=" N MET F 600 " --> pdb=" O GLU F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 619 Processing helix chain 'F' and resid 639 through 645 removed outlier: 3.675A pdb=" N ASN F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 664 removed outlier: 3.667A pdb=" N SER F 660 " --> pdb=" O SER F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 710 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 360 removed outlier: 6.631A pdb=" N GLU A 369 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL A 359 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG A 367 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 398 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 445 removed outlier: 5.349A pdb=" N ALA A 442 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR A 454 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 444 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.756A pdb=" N ILE A 590 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A 627 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 592 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA A 629 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 594 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A 650 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 463 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 360 removed outlier: 4.175A pdb=" N GLU B 369 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL B 359 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ARG B 367 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 411 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 3.613A 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 441 Processing sheet with id=AA6, first strand: chain 'B' and resid 444 through 445 Processing sheet with id=AA7, first strand: chain 'B' and resid 627 through 629 removed outlier: 5.575A pdb=" N LEU B 463 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA9, first strand: chain 'C' and resid 354 through 361 removed outlier: 4.801A pdb=" N VAL C 356 " --> pdb=" O GLN C 371 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN C 371 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 358 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 411 " --> pdb=" O PHE C 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 455 removed outlier: 3.643A pdb=" N GLY C 444 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR C 454 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA C 442 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU C 463 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE C 652 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 497 removed outlier: 6.753A pdb=" N VAL C 592 " --> pdb=" O ILE C 627 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 356 through 361 removed outlier: 4.102A pdb=" N SER D 358 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 440 through 445 removed outlier: 5.229A pdb=" N ALA D 442 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR D 454 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 444 " --> pdb=" O ILE D 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 492 through 497 removed outlier: 6.106A pdb=" N ARG D 493 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL D 593 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE D 495 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 627 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS D 461 " --> pdb=" O THR D 648 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE D 650 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU D 463 " --> pdb=" O ILE D 650 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 354 through 361 removed outlier: 5.365A pdb=" N VAL E 356 " --> pdb=" O GLN E 371 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN E 371 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE E 370 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 440 through 445 removed outlier: 3.810A pdb=" N LEU E 443 " --> pdb=" O ILE E 452 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE E 452 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.501A pdb=" N ILE E 590 " --> pdb=" O HIS E 625 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE E 627 " --> pdb=" O ILE E 590 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL E 592 " --> pdb=" O ILE E 627 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA E 629 " --> pdb=" O VAL E 592 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL E 594 " --> pdb=" O ALA E 629 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 649 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 356 through 361 removed outlier: 3.599A pdb=" N ILE F 413 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY F 410 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 440 through 445 removed outlier: 3.880A pdb=" N LEU F 443 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE F 452 " --> pdb=" O LEU F 443 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 492 through 497 removed outlier: 6.885A pdb=" N ARG F 493 " --> pdb=" O VAL F 591 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL F 593 " --> pdb=" O ARG F 493 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE F 495 " --> pdb=" O VAL F 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 590 " --> pdb=" O HIS F 625 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 627 " --> pdb=" O ILE F 590 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL F 592 " --> pdb=" O ILE F 627 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA F 629 " --> pdb=" O VAL F 592 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL F 594 " --> pdb=" O ALA F 629 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU F 462 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR F 630 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL F 464 " --> pdb=" O THR F 630 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE F 650 " --> pdb=" O HIS F 461 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU F 463 " --> pdb=" O ILE F 650 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5269 1.33 - 1.45: 2768 1.45 - 1.57: 10985 1.57 - 1.69: 80 1.69 - 1.81: 174 Bond restraints: 19276 Sorted by residual: bond pdb=" C3' DT H 16 " pdb=" C2' DT H 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.48e+00 bond pdb=" C3' DA H 9 " pdb=" C2' DA H 9 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.47e+00 bond pdb=" C3' DT G 8 " pdb=" C2' DT G 8 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.14e+00 bond pdb=" C5' DT G 2 " pdb=" C4' DT G 2 " ideal model delta sigma weight residual 1.512 1.529 -0.017 7.00e-03 2.04e+04 5.90e+00 bond pdb=" C3' DA H 11 " pdb=" O3' DA H 11 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.62e+00 ... (remaining 19271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 25691 3.07 - 6.14: 539 6.14 - 9.20: 62 9.20 - 12.27: 13 12.27 - 15.34: 8 Bond angle restraints: 26313 Sorted by residual: angle pdb=" N ILE B 615 " pdb=" CA ILE B 615 " pdb=" C ILE B 615 " ideal model delta sigma weight residual 112.17 105.43 6.74 9.50e-01 1.11e+00 5.03e+01 angle pdb=" C MET F 459 " pdb=" N PRO F 460 " pdb=" CD PRO F 460 " ideal model delta sigma weight residual 120.60 105.26 15.34 2.20e+00 2.07e-01 4.86e+01 angle pdb=" C MET F 459 " pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 127.00 142.34 -15.34 2.40e+00 1.74e-01 4.08e+01 angle pdb=" C MET B 459 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 120.60 106.99 13.61 2.20e+00 2.07e-01 3.83e+01 angle pdb=" C MET D 459 " pdb=" N PRO D 460 " pdb=" CD PRO D 460 " ideal model delta sigma weight residual 120.60 108.38 12.22 2.20e+00 2.07e-01 3.08e+01 ... (remaining 26308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 11635 35.89 - 71.78: 218 71.78 - 107.66: 4 107.66 - 143.55: 4 143.55 - 179.44: 3 Dihedral angle restraints: 11864 sinusoidal: 5063 harmonic: 6801 Sorted by residual: dihedral pdb=" O2A ADP D 801 " pdb=" O3A ADP D 801 " pdb=" PA ADP D 801 " pdb=" PB ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 120.56 179.44 1 2.00e+01 2.50e-03 4.80e+01 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 96.97 -156.97 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual -60.00 83.57 -143.56 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 11861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2539 0.075 - 0.150: 547 0.150 - 0.226: 41 0.226 - 0.301: 9 0.301 - 0.376: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CG LEU B 550 " pdb=" CB LEU B 550 " pdb=" CD1 LEU B 550 " pdb=" CD2 LEU B 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE B 452 " pdb=" CA ILE B 452 " pdb=" CG1 ILE B 452 " pdb=" CG2 ILE B 452 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE D 638 " pdb=" CA ILE D 638 " pdb=" CG1 ILE D 638 " pdb=" CG2 ILE D 638 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 3137 not shown) Planarity restraints: 3226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 459 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO B 460 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 569 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO B 570 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 632 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO C 633 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 633 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 633 " -0.034 5.00e-02 4.00e+02 ... (remaining 3223 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3151 2.76 - 3.30: 17618 3.30 - 3.83: 31836 3.83 - 4.37: 35378 4.37 - 4.90: 59190 Nonbonded interactions: 147173 Sorted by model distance: nonbonded pdb=" OG SER F 660 " pdb=" O GLN F 666 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR F 539 " pdb=" O LYS F 618 " model vdw 2.241 3.040 nonbonded pdb=" OG SER F 355 " pdb=" O GLN F 371 " model vdw 2.270 3.040 nonbonded pdb=" O ILE D 483 " pdb=" OG SER D 487 " model vdw 2.295 3.040 nonbonded pdb=" OG SER C 355 " pdb=" O GLN C 371 " model vdw 2.304 3.040 ... (remaining 147168 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 587 through 720 or resid 801)) selection = chain 'B' selection = (chain 'C' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'D' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'E' and (resid 315 through 570 or resid 587 through 720 or resid 801)) selection = (chain 'F' and (resid 315 through 570 or resid 587 through 720 or resid 801)) } 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: 0.880 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.600 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.008 0.069 19276 Z= 0.371 Angle : 1.132 15.339 26313 Z= 0.605 Chirality : 0.061 0.376 3140 Planarity : 0.008 0.070 3226 Dihedral : 13.329 179.437 7454 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.15 % Allowed : 5.70 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -4.29 (0.14), residues: 2343 helix: -2.63 (0.13), residues: 873 sheet: -2.12 (0.25), residues: 394 loop : -3.29 (0.15), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 711 TYR 0.030 0.003 TYR D 507 PHE 0.025 0.003 PHE E 597 TRP 0.036 0.005 TRP A 530 HIS 0.013 0.002 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.37 (19276) covalent geometry : angle 1.13171 / 0.60 (26313) hydrogen bonds : bond 0.17131 / 11.35 ( 729) hydrogen bonds : angle 7.58101 / 5.14 ( 2068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 635 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.9094 (t-90) cc_final: 0.8235 (t-90) REVERT: A 513 LEU cc_start: 0.8782 (tt) cc_final: 0.8400 (tt) REVERT: A 517 VAL cc_start: 0.8890 (t) cc_final: 0.8368 (m) REVERT: A 521 MET cc_start: 0.7301 (pp-130) cc_final: 0.5550 (pp-130) REVERT: A 535 MET cc_start: 0.8756 (ttm) cc_final: 0.8187 (ttp) REVERT: A 602 MET cc_start: 0.9019 (mtp) cc_final: 0.8735 (mtm) REVERT: A 609 GLU cc_start: 0.8245 (tp30) cc_final: 0.7885 (tp30) REVERT: A 614 ARG cc_start: 0.8518 (tmt-80) cc_final: 0.8253 (ttp-170) REVERT: A 632 ARG cc_start: 0.8112 (ppt-90) cc_final: 0.6618 (ptt-90) REVERT: A 650 ILE cc_start: 0.9368 (mt) cc_final: 0.9099 (tt) REVERT: A 678 MET cc_start: 0.7114 (pp-130) cc_final: 0.6558 (pp-130) REVERT: A 679 LEU cc_start: 0.8642 (mm) cc_final: 0.8278 (mm) REVERT: A 695 PHE cc_start: 0.8741 (t80) cc_final: 0.8446 (t80) REVERT: A 699 ASP cc_start: 0.9214 (m-30) cc_final: 0.8903 (t70) REVERT: B 445 HIS cc_start: 0.8335 (m90) cc_final: 0.8005 (m-70) REVERT: B 519 THR cc_start: 0.8761 (m) cc_final: 0.8528 (p) REVERT: B 542 MET cc_start: 0.9140 (ttp) cc_final: 0.8726 (ttp) REVERT: B 556 LYS cc_start: 0.9404 (mmpt) cc_final: 0.8950 (ptmm) REVERT: B 600 MET cc_start: 0.8213 (mtp) cc_final: 0.7787 (mtp) REVERT: B 614 ARG cc_start: 0.7583 (mpp80) cc_final: 0.6956 (mmm-85) REVERT: B 632 ARG cc_start: 0.5756 (tmm160) cc_final: 0.5548 (tmm160) REVERT: B 699 ASP cc_start: 0.8901 (m-30) cc_final: 0.8583 (t70) REVERT: B 716 TYR cc_start: 0.8375 (m-80) cc_final: 0.8174 (m-80) REVERT: C 425 GLU cc_start: 0.9199 (tt0) cc_final: 0.8555 (tm-30) REVERT: C 507 TYR cc_start: 0.8676 (m-80) cc_final: 0.8222 (m-80) REVERT: C 631 GLN cc_start: 0.8859 (tt0) cc_final: 0.7665 (tt0) REVERT: D 318 LEU cc_start: 0.9232 (tp) cc_final: 0.8980 (mp) REVERT: D 406 LYS cc_start: 0.8984 (mttt) cc_final: 0.8642 (mtpm) REVERT: D 441 LEU cc_start: 0.9092 (mt) cc_final: 0.8827 (mt) REVERT: D 468 THR cc_start: 0.8502 (p) cc_final: 0.7816 (m) REVERT: D 479 MET cc_start: 0.9340 (mtt) cc_final: 0.8873 (mtm) REVERT: D 595 ASP cc_start: 0.8269 (t0) cc_final: 0.8042 (t0) REVERT: D 632 ARG cc_start: 0.8534 (ptt180) cc_final: 0.7892 (tpp-160) REVERT: D 641 LEU cc_start: 0.9086 (tp) cc_final: 0.8595 (mp) REVERT: D 708 TRP cc_start: 0.8608 (m100) cc_final: 0.7962 (m100) REVERT: E 459 MET cc_start: 0.9150 (mtp) cc_final: 0.8375 (mtp) REVERT: E 540 ARG cc_start: 0.8542 (mtt180) cc_final: 0.7811 (mtm-85) REVERT: E 591 VAL cc_start: 0.9615 (t) cc_final: 0.9350 (m) REVERT: E 600 MET cc_start: 0.8778 (mtt) cc_final: 0.8545 (mtt) REVERT: E 675 HIS cc_start: 0.8044 (m170) cc_final: 0.7642 (m-70) REVERT: E 678 MET cc_start: 0.8659 (mtm) cc_final: 0.8418 (mtm) REVERT: E 702 HIS cc_start: 0.8719 (m90) cc_final: 0.8155 (m90) REVERT: F 339 MET cc_start: 0.9423 (tpp) cc_final: 0.9154 (tpp) REVERT: F 368 PHE cc_start: 0.9449 (m-80) cc_final: 0.9107 (m-10) REVERT: F 371 GLN cc_start: 0.9063 (tt0) cc_final: 0.8540 (tm-30) REVERT: F 431 GLU cc_start: 0.8745 (pm20) cc_final: 0.8232 (pm20) REVERT: F 601 MET cc_start: 0.7814 (tmt) cc_final: 0.6844 (tmm) REVERT: F 633 PRO cc_start: 0.8593 (Cg_exo) cc_final: 0.7504 (Cg_endo) REVERT: F 659 ASP cc_start: 0.7478 (m-30) cc_final: 0.7120 (m-30) outliers start: 3 outliers final: 0 residues processed: 636 average time/residue: 0.1578 time to fit residues: 148.3417 Evaluate side-chains 376 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0050 chunk 235 optimal weight: 30.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 HIS ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 435 HIS B 445 HIS ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 554 ASN D 617 GLN F 435 HIS ** F 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073697 restraints weight = 54892.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075545 restraints weight = 34731.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076862 restraints weight = 24827.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077783 restraints weight = 19320.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078390 restraints weight = 16078.194| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19276 Z= 0.171 Angle : 0.822 9.492 26313 Z= 0.403 Chirality : 0.050 0.316 3140 Planarity : 0.007 0.072 3226 Dihedral : 15.252 157.165 2973 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.25 % Allowed : 4.00 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -3.04 (0.16), residues: 2343 helix: -1.23 (0.16), residues: 883 sheet: -1.63 (0.26), residues: 383 loop : -2.84 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 537 TYR 0.041 0.002 TYR E 432 PHE 0.023 0.002 PHE A 553 TRP 0.023 0.002 TRP C 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (19276) covalent geometry : angle 0.82198 / 0.40 (26313) hydrogen bonds : bond 0.04901 / 3.28 ( 729) hydrogen bonds : angle 5.87455 / 4.03 ( 2068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 511 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.8710 (t-90) cc_final: 0.8434 (t-90) REVERT: A 481 LEU cc_start: 0.9679 (mm) cc_final: 0.9451 (mm) REVERT: A 595 ASP cc_start: 0.6928 (t70) cc_final: 0.6588 (t70) REVERT: A 626 LEU cc_start: 0.9684 (tp) cc_final: 0.9451 (tp) REVERT: A 675 HIS cc_start: 0.7746 (m170) cc_final: 0.7385 (m-70) REVERT: B 398 ARG cc_start: 0.7512 (ptm-80) cc_final: 0.6960 (mtm110) REVERT: B 441 LEU cc_start: 0.8020 (mt) cc_final: 0.7543 (mt) REVERT: B 445 HIS cc_start: 0.8346 (m-70) cc_final: 0.7669 (m-70) REVERT: B 447 ILE cc_start: 0.8062 (mm) cc_final: 0.7752 (mm) REVERT: B 529 ARG cc_start: 0.8638 (mpp-170) cc_final: 0.8083 (mtt-85) REVERT: B 535 MET cc_start: 0.9223 (tmm) cc_final: 0.8918 (tmm) REVERT: B 542 MET cc_start: 0.9183 (ttp) cc_final: 0.8734 (ttp) REVERT: B 556 LYS cc_start: 0.9320 (mmpt) cc_final: 0.8867 (ptmm) REVERT: B 664 LEU cc_start: 0.6898 (tp) cc_final: 0.6372 (tp) REVERT: B 665 ASP cc_start: 0.6698 (m-30) cc_final: 0.6423 (m-30) REVERT: C 420 MET cc_start: 0.7699 (tmm) cc_final: 0.7473 (tmm) REVERT: C 425 GLU cc_start: 0.9220 (tt0) cc_final: 0.8689 (tm-30) REVERT: C 468 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7449 (m) REVERT: C 507 TYR cc_start: 0.8520 (m-80) cc_final: 0.8302 (m-80) REVERT: C 518 VAL cc_start: 0.7774 (t) cc_final: 0.7545 (t) REVERT: C 521 MET cc_start: 0.7251 (mmm) cc_final: 0.5598 (mmt) REVERT: D 369 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6784 (tt0) REVERT: D 406 LYS cc_start: 0.8877 (mttt) cc_final: 0.8317 (mtpt) REVERT: D 425 GLU cc_start: 0.8288 (tt0) cc_final: 0.7453 (tp30) REVERT: D 447 ILE cc_start: 0.9459 (pt) cc_final: 0.9163 (mp) REVERT: D 496 MET cc_start: 0.8243 (mtp) cc_final: 0.8032 (mtp) REVERT: D 595 ASP cc_start: 0.8142 (t0) cc_final: 0.7755 (t0) REVERT: D 602 MET cc_start: 0.8278 (tpt) cc_final: 0.8007 (tpp) REVERT: D 632 ARG cc_start: 0.8057 (ptt180) cc_final: 0.7737 (tpm170) REVERT: D 671 GLN cc_start: 0.8879 (mp10) cc_final: 0.8661 (mp10) REVERT: E 329 LYS cc_start: 0.8445 (mmpt) cc_final: 0.6877 (tptt) REVERT: E 369 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7623 (mt-10) REVERT: E 456 LEU cc_start: 0.9375 (tp) cc_final: 0.9080 (tp) REVERT: E 459 MET cc_start: 0.9066 (mtp) cc_final: 0.8393 (mtp) REVERT: E 538 ARG cc_start: 0.8875 (mtt-85) cc_final: 0.8629 (mtt180) REVERT: E 540 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7860 (mtm-85) REVERT: E 600 MET cc_start: 0.8427 (mtt) cc_final: 0.8198 (mtt) REVERT: E 618 LYS cc_start: 0.7911 (ttmt) cc_final: 0.6667 (ttmt) REVERT: E 650 ILE cc_start: 0.8741 (tp) cc_final: 0.8326 (tp) REVERT: E 678 MET cc_start: 0.8489 (mtm) cc_final: 0.8270 (mtm) REVERT: F 367 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8288 (ttm-80) REVERT: F 368 PHE cc_start: 0.9381 (m-80) cc_final: 0.9062 (m-10) REVERT: F 371 GLN cc_start: 0.8796 (tt0) cc_final: 0.8453 (tm-30) REVERT: F 464 VAL cc_start: 0.9114 (t) cc_final: 0.8865 (m) REVERT: F 496 MET cc_start: 0.8745 (mmm) cc_final: 0.8419 (mmm) REVERT: F 529 ARG cc_start: 0.9016 (mpt-90) cc_final: 0.8636 (mtm-85) REVERT: F 633 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.7039 (Cg_endo) REVERT: F 659 ASP cc_start: 0.7411 (m-30) cc_final: 0.6923 (m-30) outliers start: 5 outliers final: 0 residues processed: 515 average time/residue: 0.1507 time to fit residues: 116.2165 Evaluate side-chains 379 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 HIS F 435 HIS F 675 HIS F 702 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072377 restraints weight = 56483.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074222 restraints weight = 35837.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075494 restraints weight = 25537.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076384 restraints weight = 19997.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076964 restraints weight = 16711.488| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19276 Z= 0.186 Angle : 0.783 11.835 26313 Z= 0.380 Chirality : 0.049 0.235 3140 Planarity : 0.005 0.055 3226 Dihedral : 14.908 154.174 2973 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.53 (0.16), residues: 2343 helix: -0.70 (0.17), residues: 890 sheet: -1.47 (0.26), residues: 382 loop : -2.62 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 537 TYR 0.039 0.002 TYR E 432 PHE 0.015 0.002 PHE C 423 TRP 0.018 0.002 TRP A 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (19276) covalent geometry : angle 0.78267 / 0.38 (26313) hydrogen bonds : bond 0.04422 / 2.94 ( 729) hydrogen bonds : angle 5.52780 / 3.82 ( 2068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.8956 (t-90) cc_final: 0.8347 (t-90) REVERT: A 521 MET cc_start: 0.7539 (ptp) cc_final: 0.7026 (pmm) REVERT: A 542 MET cc_start: 0.8150 (mmt) cc_final: 0.7886 (mmt) REVERT: A 626 LEU cc_start: 0.9689 (tp) cc_final: 0.9452 (tp) REVERT: B 398 ARG cc_start: 0.7633 (ptm-80) cc_final: 0.7150 (mtm110) REVERT: B 445 HIS cc_start: 0.8359 (m-70) cc_final: 0.7767 (m-70) REVERT: B 447 ILE cc_start: 0.8212 (mm) cc_final: 0.7865 (mm) REVERT: B 500 LYS cc_start: 0.6361 (mttt) cc_final: 0.6108 (mttt) REVERT: B 535 MET cc_start: 0.9271 (tmm) cc_final: 0.9038 (tmm) REVERT: B 538 ARG cc_start: 0.6945 (ptp-170) cc_final: 0.6572 (mtm180) REVERT: B 542 MET cc_start: 0.9246 (ttp) cc_final: 0.8735 (ttp) REVERT: B 556 LYS cc_start: 0.9293 (mmpt) cc_final: 0.8886 (ptmm) REVERT: C 420 MET cc_start: 0.7792 (tmm) cc_final: 0.7530 (tmm) REVERT: C 425 GLU cc_start: 0.9257 (tt0) cc_final: 0.8813 (tm-30) REVERT: C 426 VAL cc_start: 0.9004 (t) cc_final: 0.8741 (t) REVERT: C 441 LEU cc_start: 0.8412 (mt) cc_final: 0.8035 (mp) REVERT: C 479 MET cc_start: 0.8914 (mtp) cc_final: 0.8703 (mtp) REVERT: C 541 LEU cc_start: 0.9254 (tp) cc_final: 0.8901 (tp) REVERT: D 369 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6351 (tt0) REVERT: D 406 LYS cc_start: 0.8943 (mttt) cc_final: 0.8349 (mtpt) REVERT: D 425 GLU cc_start: 0.8313 (tt0) cc_final: 0.7480 (tp30) REVERT: D 447 ILE cc_start: 0.9531 (pt) cc_final: 0.9131 (mp) REVERT: D 496 MET cc_start: 0.8265 (mtp) cc_final: 0.8036 (mtp) REVERT: D 521 MET cc_start: 0.8488 (mpp) cc_final: 0.7927 (mtt) REVERT: D 595 ASP cc_start: 0.8142 (t0) cc_final: 0.7888 (t0) REVERT: D 603 ILE cc_start: 0.8134 (mm) cc_final: 0.7672 (mm) REVERT: D 614 ARG cc_start: 0.8499 (mtt180) cc_final: 0.8290 (mmt90) REVERT: D 617 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8304 (tm-30) REVERT: D 632 ARG cc_start: 0.8181 (ptt180) cc_final: 0.7636 (tpm170) REVERT: D 671 GLN cc_start: 0.8868 (mp10) cc_final: 0.8627 (mp10) REVERT: E 369 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7661 (mt-10) REVERT: E 456 LEU cc_start: 0.9335 (tp) cc_final: 0.8754 (tp) REVERT: E 459 MET cc_start: 0.9103 (mtp) cc_final: 0.8195 (mtp) REVERT: E 521 MET cc_start: 0.7363 (tmm) cc_final: 0.7130 (tmm) REVERT: E 540 ARG cc_start: 0.8522 (mtt180) cc_final: 0.7955 (mtm-85) REVERT: E 618 LYS cc_start: 0.8032 (ttmt) cc_final: 0.6798 (ttmt) REVERT: E 650 ILE cc_start: 0.8993 (tp) cc_final: 0.8441 (tp) REVERT: E 675 HIS cc_start: 0.7850 (m-70) cc_final: 0.7439 (m90) REVERT: E 678 MET cc_start: 0.8451 (mtm) cc_final: 0.8241 (mtm) REVERT: F 367 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8649 (ttm-80) REVERT: F 371 GLN cc_start: 0.8710 (tt0) cc_final: 0.8366 (tm-30) REVERT: F 441 LEU cc_start: 0.9016 (mt) cc_final: 0.8781 (mt) REVERT: F 479 MET cc_start: 0.9079 (mtm) cc_final: 0.8736 (mtm) REVERT: F 496 MET cc_start: 0.8706 (mmm) cc_final: 0.8399 (mmm) REVERT: F 500 LYS cc_start: 0.7710 (pttt) cc_final: 0.7026 (pttt) REVERT: F 601 MET cc_start: 0.7500 (tmm) cc_final: 0.6848 (tmm) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.1394 time to fit residues: 96.8278 Evaluate side-chains 351 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 31 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN C 415 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN E 477 ASN F 435 HIS F 645 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.072709 restraints weight = 56030.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.074555 restraints weight = 35406.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075859 restraints weight = 25173.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076754 restraints weight = 19547.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077383 restraints weight = 16285.896| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19276 Z= 0.178 Angle : 0.780 10.860 26313 Z= 0.376 Chirality : 0.048 0.255 3140 Planarity : 0.005 0.060 3226 Dihedral : 14.724 154.707 2973 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.27 (0.17), residues: 2343 helix: -0.48 (0.17), residues: 896 sheet: -1.27 (0.25), residues: 402 loop : -2.53 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 529 TYR 0.023 0.002 TYR D 432 PHE 0.017 0.001 PHE A 553 TRP 0.015 0.002 TRP B 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (19276) covalent geometry : angle 0.78024 / 0.38 (26313) hydrogen bonds : bond 0.04210 / 2.81 ( 729) hydrogen bonds : angle 5.43385 / 3.74 ( 2068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.8819 (t-90) cc_final: 0.8304 (t-90) REVERT: A 542 MET cc_start: 0.8071 (mmt) cc_final: 0.7814 (mmt) REVERT: A 620 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8329 (ttt180) REVERT: A 626 LEU cc_start: 0.9666 (tp) cc_final: 0.9455 (tp) REVERT: B 398 ARG cc_start: 0.7684 (ptm-80) cc_final: 0.7175 (mtm110) REVERT: B 419 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 445 HIS cc_start: 0.8378 (m-70) cc_final: 0.7709 (m-70) REVERT: B 447 ILE cc_start: 0.8254 (mm) cc_final: 0.7908 (mm) REVERT: B 519 THR cc_start: 0.8391 (p) cc_final: 0.8186 (p) REVERT: B 529 ARG cc_start: 0.8707 (mpp-170) cc_final: 0.8408 (mtt-85) REVERT: B 535 MET cc_start: 0.9200 (tmm) cc_final: 0.8935 (tmm) REVERT: B 542 MET cc_start: 0.9205 (ttp) cc_final: 0.8093 (ttp) REVERT: B 553 PHE cc_start: 0.8108 (t80) cc_final: 0.6806 (t80) REVERT: B 556 LYS cc_start: 0.9295 (mmpt) cc_final: 0.8861 (ptmm) REVERT: C 420 MET cc_start: 0.7882 (tmm) cc_final: 0.7518 (tmm) REVERT: C 425 GLU cc_start: 0.9235 (tt0) cc_final: 0.8822 (tm-30) REVERT: C 426 VAL cc_start: 0.8993 (t) cc_final: 0.8720 (t) REVERT: C 481 LEU cc_start: 0.8844 (mp) cc_final: 0.8426 (mp) REVERT: C 541 LEU cc_start: 0.9142 (tp) cc_final: 0.8819 (tp) REVERT: C 617 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7960 (tp40) REVERT: D 369 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6350 (tt0) REVERT: D 406 LYS cc_start: 0.8940 (mttt) cc_final: 0.8348 (mtpt) REVERT: D 425 GLU cc_start: 0.8248 (tt0) cc_final: 0.7414 (tp30) REVERT: D 447 ILE cc_start: 0.9529 (pt) cc_final: 0.9107 (mp) REVERT: D 496 MET cc_start: 0.8249 (mtp) cc_final: 0.7999 (mtp) REVERT: D 521 MET cc_start: 0.8444 (mpp) cc_final: 0.8051 (mtt) REVERT: D 595 ASP cc_start: 0.8203 (t0) cc_final: 0.7934 (t0) REVERT: D 599 ASP cc_start: 0.8237 (m-30) cc_final: 0.7980 (m-30) REVERT: D 602 MET cc_start: 0.8322 (tmm) cc_final: 0.8095 (tpp) REVERT: D 632 ARG cc_start: 0.8183 (ptt180) cc_final: 0.7585 (tpm170) REVERT: D 671 GLN cc_start: 0.8925 (mp10) cc_final: 0.8629 (mp10) REVERT: E 369 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7452 (mt-10) REVERT: E 422 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7874 (mmm-85) REVERT: E 459 MET cc_start: 0.9085 (mtp) cc_final: 0.8399 (mtp) REVERT: E 540 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7919 (mtm-85) REVERT: E 601 MET cc_start: 0.8517 (tpp) cc_final: 0.8289 (mmm) REVERT: E 618 LYS cc_start: 0.8097 (ttmt) cc_final: 0.6781 (ttmt) REVERT: E 650 ILE cc_start: 0.8936 (tp) cc_final: 0.8627 (tp) REVERT: E 675 HIS cc_start: 0.7794 (m-70) cc_final: 0.7433 (m90) REVERT: F 371 GLN cc_start: 0.8703 (tt0) cc_final: 0.8220 (tm-30) REVERT: F 418 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7752 (ttp-170) REVERT: F 441 LEU cc_start: 0.8983 (mt) cc_final: 0.8776 (mt) REVERT: F 479 MET cc_start: 0.9088 (mtm) cc_final: 0.8729 (mtm) REVERT: F 496 MET cc_start: 0.8693 (mmm) cc_final: 0.8397 (mmm) REVERT: F 500 LYS cc_start: 0.7860 (pttt) cc_final: 0.7341 (pttt) REVERT: F 659 ASP cc_start: 0.7365 (m-30) cc_final: 0.7135 (m-30) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.1371 time to fit residues: 94.4010 Evaluate side-chains 343 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 207 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN F 435 HIS F 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.070900 restraints weight = 56529.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.072688 restraints weight = 35891.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.073947 restraints weight = 25639.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074821 restraints weight = 20006.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075380 restraints weight = 16681.478| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 19276 Z= 0.258 Angle : 0.829 11.153 26313 Z= 0.402 Chirality : 0.050 0.244 3140 Planarity : 0.006 0.058 3226 Dihedral : 14.667 158.499 2973 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.13 (0.17), residues: 2343 helix: -0.43 (0.17), residues: 912 sheet: -1.20 (0.25), residues: 400 loop : -2.40 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 529 TYR 0.034 0.003 TYR C 507 PHE 0.018 0.002 PHE A 485 TRP 0.015 0.002 TRP B 530 HIS 0.008 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.26 (19276) covalent geometry : angle 0.82862 / 0.40 (26313) hydrogen bonds : bond 0.04405 / 2.93 ( 729) hydrogen bonds : angle 5.54249 / 3.81 ( 2068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.9011 (t-90) cc_final: 0.8594 (t-90) REVERT: A 500 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8091 (mtmt) REVERT: A 521 MET cc_start: 0.7980 (ptp) cc_final: 0.6271 (pmm) REVERT: A 542 MET cc_start: 0.8090 (mmt) cc_final: 0.7882 (mmt) REVERT: A 595 ASP cc_start: 0.6795 (t70) cc_final: 0.6433 (t70) REVERT: A 601 MET cc_start: 0.7539 (tmm) cc_final: 0.7180 (tmm) REVERT: A 626 LEU cc_start: 0.9669 (tp) cc_final: 0.9423 (tp) REVERT: B 398 ARG cc_start: 0.7739 (ptm-80) cc_final: 0.7426 (mtm110) REVERT: B 419 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7295 (tm-30) REVERT: B 445 HIS cc_start: 0.8446 (m-70) cc_final: 0.7780 (m-70) REVERT: B 447 ILE cc_start: 0.8380 (mm) cc_final: 0.8014 (mm) REVERT: B 529 ARG cc_start: 0.8751 (mpp-170) cc_final: 0.8451 (mtt-85) REVERT: B 535 MET cc_start: 0.9238 (tmm) cc_final: 0.8958 (tmm) REVERT: B 542 MET cc_start: 0.9187 (ttp) cc_final: 0.7808 (ttp) REVERT: B 553 PHE cc_start: 0.8291 (t80) cc_final: 0.7143 (t80) REVERT: C 420 MET cc_start: 0.7976 (tmm) cc_final: 0.7633 (tmm) REVERT: C 425 GLU cc_start: 0.9252 (tt0) cc_final: 0.8854 (tm-30) REVERT: C 426 VAL cc_start: 0.9051 (t) cc_final: 0.8773 (t) REVERT: C 441 LEU cc_start: 0.8317 (mp) cc_final: 0.7877 (mp) REVERT: C 541 LEU cc_start: 0.9117 (tp) cc_final: 0.8698 (tp) REVERT: D 369 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7031 (tt0) REVERT: D 406 LYS cc_start: 0.8976 (mttt) cc_final: 0.8675 (mtpt) REVERT: D 425 GLU cc_start: 0.8272 (tt0) cc_final: 0.7477 (tp30) REVERT: D 447 ILE cc_start: 0.9569 (pt) cc_final: 0.9099 (mp) REVERT: D 496 MET cc_start: 0.8245 (mtp) cc_final: 0.7725 (ttt) REVERT: D 521 MET cc_start: 0.8526 (mpp) cc_final: 0.8279 (mpp) REVERT: D 595 ASP cc_start: 0.8132 (t0) cc_final: 0.7932 (t0) REVERT: D 602 MET cc_start: 0.8318 (tmm) cc_final: 0.7793 (tmm) REVERT: D 632 ARG cc_start: 0.8351 (ptt180) cc_final: 0.7722 (tpm170) REVERT: E 432 TYR cc_start: 0.8825 (t80) cc_final: 0.8533 (t80) REVERT: E 459 MET cc_start: 0.9126 (mtp) cc_final: 0.8418 (mtp) REVERT: E 540 ARG cc_start: 0.8346 (mtt180) cc_final: 0.7868 (mtm-85) REVERT: E 618 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7764 (ttmt) REVERT: E 675 HIS cc_start: 0.7782 (m-70) cc_final: 0.7492 (m90) REVERT: F 371 GLN cc_start: 0.8651 (tt0) cc_final: 0.8350 (tm-30) REVERT: F 378 VAL cc_start: 0.9045 (t) cc_final: 0.8773 (p) REVERT: F 418 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.7355 (ttp-170) REVERT: F 441 LEU cc_start: 0.8970 (mt) cc_final: 0.8689 (mt) REVERT: F 479 MET cc_start: 0.9112 (mtm) cc_final: 0.8746 (mtm) REVERT: F 496 MET cc_start: 0.8661 (mmm) cc_final: 0.8459 (mmm) REVERT: F 641 LEU cc_start: 0.8969 (mp) cc_final: 0.7900 (mp) REVERT: F 659 ASP cc_start: 0.7414 (m-30) cc_final: 0.7160 (m-30) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1355 time to fit residues: 85.0449 Evaluate side-chains 324 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS F 617 GLN F 666 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.072706 restraints weight = 55880.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074444 restraints weight = 36271.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075627 restraints weight = 26221.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076497 restraints weight = 20687.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077099 restraints weight = 17344.968| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19276 Z= 0.175 Angle : 0.788 13.204 26313 Z= 0.380 Chirality : 0.049 0.283 3140 Planarity : 0.005 0.068 3226 Dihedral : 14.547 159.597 2973 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.88 (0.17), residues: 2343 helix: -0.17 (0.17), residues: 910 sheet: -1.05 (0.26), residues: 379 loop : -2.30 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 529 TYR 0.031 0.002 TYR C 507 PHE 0.014 0.002 PHE A 553 TRP 0.015 0.002 TRP B 530 HIS 0.005 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (19276) covalent geometry : angle 0.78808 / 0.38 (26313) hydrogen bonds : bond 0.04147 / 2.79 ( 729) hydrogen bonds : angle 5.36988 / 3.72 ( 2068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 MET cc_start: 0.8066 (mmt) cc_final: 0.7788 (mmt) REVERT: A 626 LEU cc_start: 0.9653 (tp) cc_final: 0.9444 (tp) REVERT: A 632 ARG cc_start: 0.8492 (ptp-110) cc_final: 0.8269 (ptp-170) REVERT: A 699 ASP cc_start: 0.8643 (t0) cc_final: 0.8412 (t70) REVERT: B 419 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7378 (tm-30) REVERT: B 445 HIS cc_start: 0.8338 (m-70) cc_final: 0.7712 (m-70) REVERT: B 447 ILE cc_start: 0.8370 (mm) cc_final: 0.8139 (mp) REVERT: B 538 ARG cc_start: 0.7186 (ptp-170) cc_final: 0.6600 (mtm180) REVERT: B 542 MET cc_start: 0.9184 (ttp) cc_final: 0.8560 (ttp) REVERT: B 545 MET cc_start: 0.7946 (mpp) cc_final: 0.7512 (mpp) REVERT: B 556 LYS cc_start: 0.9260 (mmpt) cc_final: 0.8920 (pttp) REVERT: C 420 MET cc_start: 0.8005 (tmm) cc_final: 0.7628 (tmm) REVERT: C 425 GLU cc_start: 0.9225 (tt0) cc_final: 0.8840 (tm-30) REVERT: C 426 VAL cc_start: 0.9033 (t) cc_final: 0.8776 (t) REVERT: C 522 LYS cc_start: 0.8463 (mmpt) cc_final: 0.7527 (mtmt) REVERT: C 535 MET cc_start: 0.9140 (tmm) cc_final: 0.8912 (tmm) REVERT: C 539 TYR cc_start: 0.7126 (m-80) cc_final: 0.6911 (m-10) REVERT: C 541 LEU cc_start: 0.9075 (tp) cc_final: 0.8587 (tp) REVERT: D 369 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6951 (tt0) REVERT: D 406 LYS cc_start: 0.8994 (mttt) cc_final: 0.8677 (mtpt) REVERT: D 425 GLU cc_start: 0.8214 (tt0) cc_final: 0.7415 (tp30) REVERT: D 447 ILE cc_start: 0.9558 (pt) cc_final: 0.9104 (mp) REVERT: D 603 ILE cc_start: 0.6989 (tt) cc_final: 0.6559 (tt) REVERT: D 632 ARG cc_start: 0.8307 (ptt180) cc_final: 0.7664 (tpm170) REVERT: D 678 MET cc_start: 0.8220 (mtm) cc_final: 0.7951 (mtm) REVERT: E 432 TYR cc_start: 0.8763 (t80) cc_final: 0.8450 (t80) REVERT: E 459 MET cc_start: 0.9114 (mtp) cc_final: 0.8434 (mtp) REVERT: E 461 HIS cc_start: 0.8500 (m-70) cc_final: 0.8137 (m-70) REVERT: E 540 ARG cc_start: 0.8423 (mtt180) cc_final: 0.7842 (mtm-85) REVERT: E 670 GLU cc_start: 0.8681 (pm20) cc_final: 0.8447 (pm20) REVERT: E 675 HIS cc_start: 0.7692 (m-70) cc_final: 0.7461 (m90) REVERT: F 371 GLN cc_start: 0.8619 (tt0) cc_final: 0.8305 (tm-30) REVERT: F 479 MET cc_start: 0.9050 (mtm) cc_final: 0.8805 (mtm) REVERT: F 480 LEU cc_start: 0.9644 (mm) cc_final: 0.9414 (mt) REVERT: F 496 MET cc_start: 0.8703 (mmm) cc_final: 0.8427 (mmm) REVERT: F 500 LYS cc_start: 0.8403 (pttt) cc_final: 0.8202 (pttt) REVERT: F 601 MET cc_start: 0.7742 (tmm) cc_final: 0.7387 (tmm) REVERT: F 641 LEU cc_start: 0.8929 (mp) cc_final: 0.7937 (mp) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.1376 time to fit residues: 88.5024 Evaluate side-chains 326 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 223 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 196 optimal weight: 0.1980 chunk 218 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 4 optimal weight: 0.0070 chunk 117 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN E 415 ASN F 435 HIS F 617 GLN F 666 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.074664 restraints weight = 55733.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076429 restraints weight = 35613.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.077662 restraints weight = 25601.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078529 restraints weight = 20036.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079088 restraints weight = 16762.815| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19276 Z= 0.134 Angle : 0.771 11.452 26313 Z= 0.368 Chirality : 0.049 0.289 3140 Planarity : 0.005 0.051 3226 Dihedral : 14.349 156.881 2973 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.66 (0.17), residues: 2343 helix: 0.04 (0.18), residues: 919 sheet: -0.92 (0.26), residues: 380 loop : -2.24 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 529 TYR 0.031 0.002 TYR C 507 PHE 0.016 0.002 PHE A 695 TRP 0.016 0.002 TRP B 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (19276) covalent geometry : angle 0.77138 / 0.37 (26313) hydrogen bonds : bond 0.03835 / 2.60 ( 729) hydrogen bonds : angle 5.21477 / 3.62 ( 2068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8373 (pm20) cc_final: 0.8136 (mp0) REVERT: A 501 MET cc_start: 0.8910 (mpp) cc_final: 0.8465 (mpp) REVERT: A 609 GLU cc_start: 0.8125 (tp30) cc_final: 0.7893 (tp30) REVERT: A 626 LEU cc_start: 0.9666 (tp) cc_final: 0.9460 (tp) REVERT: A 632 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.8248 (ptp-110) REVERT: A 695 PHE cc_start: 0.8367 (t80) cc_final: 0.8118 (t80) REVERT: A 699 ASP cc_start: 0.8580 (t0) cc_final: 0.8325 (t70) REVERT: B 419 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 445 HIS cc_start: 0.8250 (m-70) cc_final: 0.7714 (m-70) REVERT: B 447 ILE cc_start: 0.8306 (mm) cc_final: 0.7990 (mm) REVERT: B 542 MET cc_start: 0.9133 (ttp) cc_final: 0.8738 (ttp) REVERT: B 545 MET cc_start: 0.7940 (mpp) cc_final: 0.7359 (mpp) REVERT: B 556 LYS cc_start: 0.9240 (mmpt) cc_final: 0.8912 (pttp) REVERT: C 420 MET cc_start: 0.8018 (tmm) cc_final: 0.7650 (tmm) REVERT: C 425 GLU cc_start: 0.9188 (tt0) cc_final: 0.8833 (tm-30) REVERT: C 441 LEU cc_start: 0.8404 (mp) cc_final: 0.7889 (mp) REVERT: C 522 LYS cc_start: 0.8400 (mmpt) cc_final: 0.7470 (mtmt) REVERT: C 541 LEU cc_start: 0.9073 (tp) cc_final: 0.8448 (tp) REVERT: D 318 LEU cc_start: 0.8614 (mp) cc_final: 0.8256 (tp) REVERT: D 369 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6631 (tt0) REVERT: D 406 LYS cc_start: 0.8972 (mttt) cc_final: 0.8465 (mtpm) REVERT: D 425 GLU cc_start: 0.8090 (tt0) cc_final: 0.7287 (tp30) REVERT: D 426 VAL cc_start: 0.9047 (t) cc_final: 0.8806 (t) REVERT: D 447 ILE cc_start: 0.9545 (pt) cc_final: 0.9092 (mp) REVERT: D 496 MET cc_start: 0.8130 (mtp) cc_final: 0.7888 (mtp) REVERT: D 601 MET cc_start: 0.8385 (tmm) cc_final: 0.8165 (tmm) REVERT: D 632 ARG cc_start: 0.8146 (ptt180) cc_final: 0.7562 (tpm170) REVERT: E 369 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7259 (mt-10) REVERT: E 459 MET cc_start: 0.9043 (mtp) cc_final: 0.8485 (mtp) REVERT: E 461 HIS cc_start: 0.8427 (m-70) cc_final: 0.8205 (m-70) REVERT: E 521 MET cc_start: 0.7368 (tmm) cc_final: 0.6606 (tmm) REVERT: E 540 ARG cc_start: 0.8432 (mtt180) cc_final: 0.7963 (mtm-85) REVERT: E 650 ILE cc_start: 0.9006 (tp) cc_final: 0.8298 (tp) REVERT: E 670 GLU cc_start: 0.8579 (pm20) cc_final: 0.8338 (pm20) REVERT: E 675 HIS cc_start: 0.7646 (m-70) cc_final: 0.7358 (m90) REVERT: E 678 MET cc_start: 0.7925 (mtp) cc_final: 0.7608 (mtp) REVERT: F 334 GLU cc_start: 0.8279 (tp30) cc_final: 0.8053 (tp30) REVERT: F 344 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8093 (mt-10) REVERT: F 371 GLN cc_start: 0.8631 (tt0) cc_final: 0.8184 (tm-30) REVERT: F 496 MET cc_start: 0.8690 (mmm) cc_final: 0.8416 (mmm) REVERT: F 601 MET cc_start: 0.7645 (tmm) cc_final: 0.7339 (tmm) REVERT: F 641 LEU cc_start: 0.8891 (mp) cc_final: 0.8184 (mp) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1360 time to fit residues: 91.5068 Evaluate side-chains 337 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 97 optimal weight: 0.0020 chunk 1 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN D 666 GLN F 617 GLN F 666 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.071715 restraints weight = 56284.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073542 restraints weight = 35491.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074744 restraints weight = 25256.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075668 restraints weight = 19787.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076304 restraints weight = 16456.603| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19276 Z= 0.216 Angle : 0.803 11.555 26313 Z= 0.384 Chirality : 0.049 0.289 3140 Planarity : 0.005 0.056 3226 Dihedral : 14.253 150.899 2973 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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 (0.18), residues: 2343 helix: 0.01 (0.17), residues: 927 sheet: -0.88 (0.27), residues: 379 loop : -2.07 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 529 TYR 0.029 0.002 TYR C 507 PHE 0.015 0.002 PHE A 485 TRP 0.016 0.002 TRP B 530 HIS 0.008 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (19276) covalent geometry : angle 0.80332 / 0.38 (26313) hydrogen bonds : bond 0.04048 / 2.73 ( 729) hydrogen bonds : angle 5.30089 / 3.68 ( 2068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 GLU cc_start: 0.7881 (tp30) cc_final: 0.7631 (tp30) REVERT: A 521 MET cc_start: 0.7290 (pmm) cc_final: 0.6891 (pmm) REVERT: A 628 LEU cc_start: 0.9661 (mt) cc_final: 0.9430 (mt) REVERT: A 632 ARG cc_start: 0.8645 (ptp-110) cc_final: 0.8343 (ptp-170) REVERT: A 699 ASP cc_start: 0.8628 (t0) cc_final: 0.8348 (t70) REVERT: B 419 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 445 HIS cc_start: 0.8315 (m-70) cc_final: 0.7807 (m-70) REVERT: B 447 ILE cc_start: 0.8380 (mm) cc_final: 0.8138 (mp) REVERT: B 535 MET cc_start: 0.9372 (tmm) cc_final: 0.9113 (tmm) REVERT: B 542 MET cc_start: 0.9075 (ttp) cc_final: 0.8353 (ttp) REVERT: B 545 MET cc_start: 0.7902 (mpp) cc_final: 0.7501 (mpp) REVERT: C 420 MET cc_start: 0.8030 (tmm) cc_final: 0.7601 (tmm) REVERT: C 425 GLU cc_start: 0.9296 (tt0) cc_final: 0.8808 (tm-30) REVERT: C 445 HIS cc_start: 0.8353 (m-70) cc_final: 0.7075 (m170) REVERT: C 479 MET cc_start: 0.9019 (mtp) cc_final: 0.8647 (mtm) REVERT: C 522 LYS cc_start: 0.8435 (mmpt) cc_final: 0.7463 (mtmt) REVERT: C 541 LEU cc_start: 0.9096 (tp) cc_final: 0.8503 (tp) REVERT: D 318 LEU cc_start: 0.8683 (mp) cc_final: 0.8333 (tp) REVERT: D 369 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6855 (tt0) REVERT: D 406 LYS cc_start: 0.9012 (mttt) cc_final: 0.8527 (mtpm) REVERT: D 425 GLU cc_start: 0.8175 (tt0) cc_final: 0.7423 (tp30) REVERT: D 447 ILE cc_start: 0.9579 (pt) cc_final: 0.9158 (mp) REVERT: D 479 MET cc_start: 0.9012 (mtm) cc_final: 0.8573 (mtm) REVERT: D 521 MET cc_start: 0.8496 (mpp) cc_final: 0.8087 (mtt) REVERT: D 603 ILE cc_start: 0.6753 (tt) cc_final: 0.6431 (tt) REVERT: D 631 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8217 (mm-40) REVERT: D 632 ARG cc_start: 0.8385 (ptt180) cc_final: 0.7753 (tpm170) REVERT: E 369 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 459 MET cc_start: 0.9123 (mtp) cc_final: 0.8420 (mtp) REVERT: E 461 HIS cc_start: 0.8686 (m-70) cc_final: 0.8102 (m-70) REVERT: E 540 ARG cc_start: 0.8437 (mtt180) cc_final: 0.7916 (mtm-85) REVERT: E 675 HIS cc_start: 0.7704 (m-70) cc_final: 0.7344 (m90) REVERT: E 678 MET cc_start: 0.7956 (mtp) cc_final: 0.7579 (mtp) REVERT: F 371 GLN cc_start: 0.8622 (tt0) cc_final: 0.8302 (tm-30) REVERT: F 496 MET cc_start: 0.8752 (mmm) cc_final: 0.8509 (mmm) REVERT: F 641 LEU cc_start: 0.8927 (mp) cc_final: 0.7977 (mp) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1281 time to fit residues: 80.5803 Evaluate side-chains 310 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 168 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS F 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.073480 restraints weight = 55524.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075351 restraints weight = 34942.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.076650 restraints weight = 24767.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077556 restraints weight = 19216.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.078138 restraints weight = 15976.790| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19276 Z= 0.149 Angle : 0.780 11.981 26313 Z= 0.371 Chirality : 0.049 0.260 3140 Planarity : 0.005 0.055 3226 Dihedral : 14.097 143.531 2973 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.42 (0.18), residues: 2343 helix: 0.16 (0.18), residues: 928 sheet: -0.88 (0.27), residues: 398 loop : -2.00 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 529 TYR 0.029 0.002 TYR C 507 PHE 0.020 0.002 PHE D 553 TRP 0.018 0.002 TRP B 530 HIS 0.012 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (19276) covalent geometry : angle 0.77981 / 0.37 (26313) hydrogen bonds : bond 0.03790 / 2.57 ( 729) hydrogen bonds : angle 5.21111 / 3.63 ( 2068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.7351 (pmm) cc_final: 0.6958 (pmm) REVERT: A 601 MET cc_start: 0.7450 (tmm) cc_final: 0.6906 (tmm) REVERT: A 632 ARG cc_start: 0.8650 (ptp-110) cc_final: 0.8346 (ptp-170) REVERT: A 699 ASP cc_start: 0.8608 (t0) cc_final: 0.8348 (t70) REVERT: B 419 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 445 HIS cc_start: 0.8310 (m-70) cc_final: 0.7729 (m-70) REVERT: B 446 ASP cc_start: 0.8038 (m-30) cc_final: 0.7765 (m-30) REVERT: B 447 ILE cc_start: 0.8389 (mm) cc_final: 0.8165 (mp) REVERT: B 535 MET cc_start: 0.9319 (tmm) cc_final: 0.8935 (tmm) REVERT: B 542 MET cc_start: 0.9081 (ttp) cc_final: 0.8317 (ttp) REVERT: B 556 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8911 (pttp) REVERT: C 420 MET cc_start: 0.8048 (tmm) cc_final: 0.7668 (tmm) REVERT: C 425 GLU cc_start: 0.9296 (tt0) cc_final: 0.8798 (tm-30) REVERT: C 445 HIS cc_start: 0.8356 (m-70) cc_final: 0.7055 (m170) REVERT: C 479 MET cc_start: 0.8977 (mtp) cc_final: 0.8766 (mtm) REVERT: C 522 LYS cc_start: 0.8409 (mmpt) cc_final: 0.7438 (mtmt) REVERT: D 318 LEU cc_start: 0.8636 (mp) cc_final: 0.8290 (tp) REVERT: D 369 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6738 (tt0) REVERT: D 406 LYS cc_start: 0.8988 (mttt) cc_final: 0.8504 (mtpm) REVERT: D 425 GLU cc_start: 0.8148 (tt0) cc_final: 0.7339 (tp30) REVERT: D 426 VAL cc_start: 0.9087 (t) cc_final: 0.8811 (t) REVERT: D 447 ILE cc_start: 0.9571 (pt) cc_final: 0.9165 (mp) REVERT: D 479 MET cc_start: 0.8996 (mtm) cc_final: 0.8596 (mtm) REVERT: D 495 ILE cc_start: 0.8938 (mm) cc_final: 0.8672 (mm) REVERT: D 496 MET cc_start: 0.8347 (mtp) cc_final: 0.7983 (mpp) REVERT: D 521 MET cc_start: 0.8466 (mpp) cc_final: 0.8057 (mtt) REVERT: D 555 ARG cc_start: 0.8271 (tpt170) cc_final: 0.8039 (tpt170) REVERT: D 603 ILE cc_start: 0.6750 (tt) cc_final: 0.6123 (tt) REVERT: D 631 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8221 (mm-40) REVERT: D 632 ARG cc_start: 0.8244 (ptt180) cc_final: 0.7664 (tpm170) REVERT: E 369 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7292 (mt-10) REVERT: E 459 MET cc_start: 0.9020 (mtp) cc_final: 0.8363 (mtp) REVERT: E 461 HIS cc_start: 0.8673 (m-70) cc_final: 0.8123 (m-70) REVERT: E 521 MET cc_start: 0.7515 (tmm) cc_final: 0.6875 (tmm) REVERT: E 540 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7946 (mtm-85) REVERT: E 650 ILE cc_start: 0.9024 (tp) cc_final: 0.8423 (tp) REVERT: E 675 HIS cc_start: 0.7614 (m-70) cc_final: 0.7366 (m90) REVERT: F 334 GLU cc_start: 0.8336 (tp30) cc_final: 0.8127 (tp30) REVERT: F 371 GLN cc_start: 0.8598 (tt0) cc_final: 0.8269 (tm-30) REVERT: F 419 GLN cc_start: 0.8957 (tt0) cc_final: 0.8435 (tm-30) REVERT: F 496 MET cc_start: 0.8742 (mmm) cc_final: 0.8480 (mmm) REVERT: F 500 LYS cc_start: 0.8024 (pttt) cc_final: 0.7726 (pttt) REVERT: F 601 MET cc_start: 0.7935 (tmm) cc_final: 0.7663 (tmm) REVERT: F 641 LEU cc_start: 0.8883 (mp) cc_final: 0.7959 (mp) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1305 time to fit residues: 83.7370 Evaluate side-chains 325 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 33 optimal weight: 2.9990 chunk 142 optimal weight: 0.0570 chunk 182 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 224 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS F 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.073251 restraints weight = 56146.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075099 restraints weight = 35671.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076349 restraints weight = 25477.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077258 restraints weight = 19953.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077841 restraints weight = 16636.063| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19276 Z= 0.156 Angle : 0.775 11.631 26313 Z= 0.369 Chirality : 0.048 0.254 3140 Planarity : 0.005 0.073 3226 Dihedral : 13.977 144.054 2973 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.32 (0.18), residues: 2343 helix: 0.22 (0.18), residues: 931 sheet: -0.82 (0.26), residues: 398 loop : -1.93 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 529 TYR 0.029 0.002 TYR C 507 PHE 0.020 0.002 PHE E 652 TRP 0.019 0.002 TRP B 530 HIS 0.012 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (19276) covalent geometry : angle 0.77518 / 0.37 (26313) hydrogen bonds : bond 0.03785 / 2.58 ( 729) hydrogen bonds : angle 5.16599 / 3.60 ( 2068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8477 (pm20) cc_final: 0.8239 (mp0) REVERT: A 628 LEU cc_start: 0.9647 (mt) cc_final: 0.9446 (mt) REVERT: A 632 ARG cc_start: 0.8637 (ptp-110) cc_final: 0.8344 (ptp-170) REVERT: B 419 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 445 HIS cc_start: 0.8232 (m-70) cc_final: 0.7743 (m-70) REVERT: B 535 MET cc_start: 0.9158 (tmm) cc_final: 0.8847 (tmm) REVERT: B 542 MET cc_start: 0.9039 (ttp) cc_final: 0.8497 (ttp) REVERT: B 556 LYS cc_start: 0.9243 (mmpt) cc_final: 0.8911 (pttp) REVERT: C 420 MET cc_start: 0.8048 (tmm) cc_final: 0.7661 (tmm) REVERT: C 425 GLU cc_start: 0.9284 (tt0) cc_final: 0.8793 (tm-30) REVERT: C 445 HIS cc_start: 0.8311 (m-70) cc_final: 0.7056 (m170) REVERT: C 479 MET cc_start: 0.8941 (mtp) cc_final: 0.8705 (mtm) REVERT: C 521 MET cc_start: 0.6147 (mmm) cc_final: 0.5941 (mmp) REVERT: C 522 LYS cc_start: 0.8371 (mmpt) cc_final: 0.7420 (mtmt) REVERT: C 541 LEU cc_start: 0.9135 (tp) cc_final: 0.8905 (tp) REVERT: C 545 MET cc_start: 0.8425 (mmp) cc_final: 0.8219 (mmp) REVERT: C 661 ARG cc_start: 0.8656 (ptp-110) cc_final: 0.8442 (ttm110) REVERT: D 318 LEU cc_start: 0.8661 (mp) cc_final: 0.8316 (tp) REVERT: D 369 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7138 (mt-10) REVERT: D 425 GLU cc_start: 0.8121 (tt0) cc_final: 0.7305 (tp30) REVERT: D 426 VAL cc_start: 0.9052 (t) cc_final: 0.8801 (t) REVERT: D 447 ILE cc_start: 0.9569 (pt) cc_final: 0.9148 (mp) REVERT: D 479 MET cc_start: 0.8952 (mtm) cc_final: 0.8505 (mtm) REVERT: D 599 ASP cc_start: 0.8459 (m-30) cc_final: 0.8083 (m-30) REVERT: D 602 MET cc_start: 0.7905 (tmm) cc_final: 0.7702 (tmm) REVERT: D 632 ARG cc_start: 0.8231 (ptt180) cc_final: 0.7771 (tpm170) REVERT: E 369 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7313 (mt-10) REVERT: E 456 LEU cc_start: 0.9283 (tp) cc_final: 0.9051 (tp) REVERT: E 459 MET cc_start: 0.9049 (mtp) cc_final: 0.8391 (mtp) REVERT: E 461 HIS cc_start: 0.8675 (m-70) cc_final: 0.8230 (m-70) REVERT: E 521 MET cc_start: 0.7391 (tmm) cc_final: 0.6916 (tmm) REVERT: E 540 ARG cc_start: 0.8438 (mtt180) cc_final: 0.7956 (mtm-85) REVERT: E 617 GLN cc_start: 0.8263 (mm110) cc_final: 0.7835 (tp40) REVERT: E 675 HIS cc_start: 0.7679 (m-70) cc_final: 0.7374 (m90) REVERT: F 371 GLN cc_start: 0.8600 (tt0) cc_final: 0.8272 (tm-30) REVERT: F 419 GLN cc_start: 0.8971 (tt0) cc_final: 0.8489 (tm-30) REVERT: F 496 MET cc_start: 0.8742 (mmm) cc_final: 0.8523 (mmm) REVERT: F 641 LEU cc_start: 0.8882 (mp) cc_final: 0.7986 (mp) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1291 time to fit residues: 81.6872 Evaluate side-chains 322 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN F 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.072910 restraints weight = 56496.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074611 restraints weight = 36570.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.075818 restraints weight = 26645.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076644 restraints weight = 21028.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077257 restraints weight = 17717.259| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19276 Z= 0.188 Angle : 0.799 12.883 26313 Z= 0.382 Chirality : 0.049 0.254 3140 Planarity : 0.005 0.076 3226 Dihedral : 13.885 144.989 2973 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2343 helix: 0.16 (0.18), residues: 930 sheet: -0.79 (0.26), residues: 409 loop : -1.92 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 529 TYR 0.030 0.002 TYR D 539 PHE 0.017 0.002 PHE B 597 TRP 0.017 0.002 TRP B 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (19276) covalent geometry : angle 0.79915 / 0.38 (26313) hydrogen bonds : bond 0.03906 / 2.68 ( 729) hydrogen bonds : angle 5.27805 / 3.66 ( 2068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.29 seconds wall clock time: 51 minutes 58.09 seconds (3118.09 seconds total)