Starting phenix.real_space_refine on Thu Mar 5 03:49:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t8g_10400/03_2026/6t8g_10400.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8g_10400/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6t8g_10400/03_2026/6t8g_10400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8g_10400/03_2026/6t8g_10400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t8g_10400/03_2026/6t8g_10400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8g_10400/03_2026/6t8g_10400.map" } 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-dev-5986/lib/python3.9/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: 4.36, per 1000 atoms: 0.23 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: 1.47 Conformation dependent library (CDL) restraints added in 768.8 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: 2.08 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: 3.09 Time building geometry restraints manager: 1.98 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=" C SER C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 1.337 1.358 -0.021 9.80e-03 1.04e+04 4.64e+00 bond pdb=" CG1 ILE D 663 " pdb=" CD1 ILE D 663 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.14e+00 bond pdb=" CG ARG D 649 " pdb=" CD ARG D 649 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" CA LYS B 329 " pdb=" C LYS B 329 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.34e-02 5.57e+03 2.56e+00 bond pdb=" CG ARG E 390 " pdb=" CD ARG E 390 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.54e+00 ... (remaining 19271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 25696 3.07 - 6.14: 534 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: 2554 0.075 - 0.150: 532 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: 0.910 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.330 Find NCS groups from input model: 0.490 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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= 0.340 Angle : 1.121 15.339 26313 Z= 0.570 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 covalent geometry : bond 0.00767 (19276) covalent geometry : angle 1.12055 (26313) hydrogen bonds : bond 0.17131 ( 729) hydrogen bonds : angle 7.58101 ( 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 : 0.583 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: 0.8186 (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: 0.6557 (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: 0.8527 (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: 0.7891 (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: 0.7812 (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: 0.7641 (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: 0.7505 (Cg_endo) REVERT: F 659 ASP cc_start: 0.7478 (m-30) cc_final: 0.7123 (m-30) outliers start: 3 outliers final: 0 residues processed: 636 average time/residue: 0.1502 time to fit residues: 140.3358 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 : 0.673 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 645 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.074452 restraints weight = 54841.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.076324 restraints weight = 34589.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077642 restraints weight = 24642.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078547 restraints weight = 19168.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079200 restraints weight = 15968.213| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19276 Z= 0.155 Angle : 0.753 9.601 26313 Z= 0.366 Chirality : 0.047 0.270 3140 Planarity : 0.006 0.057 3226 Dihedral : 14.673 150.057 2973 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: -2.79 (0.16), residues: 2343 helix: -0.99 (0.16), residues: 886 sheet: -1.50 (0.25), residues: 396 loop : -2.75 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 649 TYR 0.031 0.002 TYR E 432 PHE 0.012 0.001 PHE A 553 TRP 0.024 0.002 TRP C 530 HIS 0.011 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00337 (19276) covalent geometry : angle 0.75344 (26313) hydrogen bonds : bond 0.04044 ( 729) hydrogen bonds : angle 5.39631 ( 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 522 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 0.688 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: 0.8773 (t-90) cc_final: 0.8484 (t-90) REVERT: A 481 LEU cc_start: 0.9710 (mm) cc_final: 0.9489 (mm) REVERT: A 595 ASP cc_start: 0.7015 (t70) cc_final: 0.6702 (t70) REVERT: A 609 GLU cc_start: 0.7967 (tp30) cc_final: 0.7588 (tp30) REVERT: A 626 LEU cc_start: 0.9672 (tp) cc_final: 0.9457 (tp) REVERT: A 678 MET cc_start: 0.7580 (ptt) cc_final: 0.7292 (ptm) REVERT: A 699 ASP cc_start: 0.8978 (m-30) cc_final: 0.8640 (t70) REVERT: B 387 ASP cc_start: 0.8779 (m-30) cc_final: 0.8557 (m-30) REVERT: B 419 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 445 HIS cc_start: 0.8314 (m-70) cc_final: 0.7766 (m-70) REVERT: B 447 ILE cc_start: 0.8090 (mm) cc_final: 0.7853 (mm) REVERT: B 529 ARG cc_start: 0.8546 (mpp-170) cc_final: 0.8058 (mtt-85) REVERT: B 535 MET cc_start: 0.9213 (tmm) cc_final: 0.8939 (tmm) REVERT: B 542 MET cc_start: 0.9218 (ttp) cc_final: 0.8744 (ttp) REVERT: B 556 LYS cc_start: 0.9264 (mmpt) cc_final: 0.8917 (pttp) REVERT: B 606 LYS cc_start: 0.8677 (mmtt) cc_final: 0.7138 (tttt) REVERT: B 664 LEU cc_start: 0.6742 (tp) cc_final: 0.6316 (tp) REVERT: B 665 ASP cc_start: 0.6551 (m-30) cc_final: 0.6205 (m-30) REVERT: B 696 VAL cc_start: 0.8626 (t) cc_final: 0.8314 (t) REVERT: C 425 GLU cc_start: 0.9220 (tt0) cc_final: 0.8789 (tm-30) REVERT: C 426 VAL cc_start: 0.8975 (t) cc_final: 0.8688 (t) REVERT: C 521 MET cc_start: 0.7254 (mmm) cc_final: 0.5950 (mmt) REVERT: C 666 GLN cc_start: 0.6560 (mp10) cc_final: 0.6210 (mp10) REVERT: D 369 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6532 (tt0) REVERT: D 406 LYS cc_start: 0.8930 (mttt) cc_final: 0.8355 (mtpt) REVERT: D 425 GLU cc_start: 0.8212 (tt0) cc_final: 0.7356 (tp30) REVERT: D 447 ILE cc_start: 0.9533 (pt) cc_final: 0.9110 (mp) REVERT: D 595 ASP cc_start: 0.8073 (t0) cc_final: 0.7666 (t0) REVERT: D 632 ARG cc_start: 0.7969 (ptt180) cc_final: 0.7573 (tpm170) REVERT: E 369 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7660 (mt-10) REVERT: E 456 LEU cc_start: 0.9316 (tp) cc_final: 0.8782 (tp) REVERT: E 459 MET cc_start: 0.9028 (mtp) cc_final: 0.8147 (mtp) REVERT: E 474 VAL cc_start: 0.9253 (t) cc_final: 0.9031 (p) REVERT: E 540 ARG cc_start: 0.8503 (mtt180) cc_final: 0.7862 (mtm-85) REVERT: E 600 MET cc_start: 0.8430 (mtt) cc_final: 0.8211 (mtt) REVERT: E 650 ILE cc_start: 0.8904 (tp) cc_final: 0.8358 (tp) REVERT: E 678 MET cc_start: 0.8391 (mtm) cc_final: 0.8132 (mtm) REVERT: E 702 HIS cc_start: 0.8673 (m90) cc_final: 0.8125 (m90) REVERT: F 371 GLN cc_start: 0.8742 (tt0) cc_final: 0.8344 (tm-30) REVERT: F 441 LEU cc_start: 0.9035 (mt) cc_final: 0.8735 (mt) REVERT: F 464 VAL cc_start: 0.9067 (t) cc_final: 0.8821 (m) REVERT: F 496 MET cc_start: 0.8749 (mmm) cc_final: 0.8468 (mmm) REVERT: F 500 LYS cc_start: 0.7707 (pttt) cc_final: 0.7166 (pttt) REVERT: F 529 ARG cc_start: 0.9056 (mpt-90) cc_final: 0.8600 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.1408 time to fit residues: 110.5399 Evaluate side-chains 363 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 7.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 233 optimal weight: 3.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 675 HIS F 360 HIS F 435 HIS F 666 GLN F 702 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.071498 restraints weight = 56203.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.073248 restraints weight = 36396.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074467 restraints weight = 26330.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075309 restraints weight = 20781.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075935 restraints weight = 17503.641| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19276 Z= 0.217 Angle : 0.784 9.901 26313 Z= 0.379 Chirality : 0.048 0.205 3140 Planarity : 0.005 0.052 3226 Dihedral : 14.458 155.440 2973 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.15 % 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: -2.27 (0.17), residues: 2343 helix: -0.47 (0.17), residues: 899 sheet: -1.32 (0.26), residues: 402 loop : -2.51 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 422 TYR 0.035 0.002 TYR E 432 PHE 0.016 0.002 PHE F 597 TRP 0.018 0.002 TRP A 530 HIS 0.009 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00487 (19276) covalent geometry : angle 0.78393 (26313) hydrogen bonds : bond 0.04156 ( 729) hydrogen bonds : angle 5.28643 ( 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 443 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.9016 (t-90) cc_final: 0.8685 (t-90) REVERT: A 600 MET cc_start: 0.8360 (mtp) cc_final: 0.8026 (mtp) REVERT: A 602 MET cc_start: 0.8432 (mtt) cc_final: 0.8178 (mtt) REVERT: A 609 GLU cc_start: 0.8148 (tp30) cc_final: 0.7944 (tp30) REVERT: A 626 LEU cc_start: 0.9671 (tp) cc_final: 0.9433 (tp) REVERT: A 650 ILE cc_start: 0.9286 (mt) cc_final: 0.8959 (mt) REVERT: A 699 ASP cc_start: 0.9042 (m-30) cc_final: 0.8691 (t70) REVERT: B 419 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 445 HIS cc_start: 0.8425 (m-70) cc_final: 0.7770 (m-70) REVERT: B 447 ILE cc_start: 0.8359 (mm) cc_final: 0.8110 (mm) REVERT: B 519 THR cc_start: 0.8246 (p) cc_final: 0.8006 (p) REVERT: B 529 ARG cc_start: 0.8618 (mpp-170) cc_final: 0.8129 (mtt-85) REVERT: B 535 MET cc_start: 0.9172 (tmm) cc_final: 0.8761 (tmm) REVERT: B 542 MET cc_start: 0.9272 (ttp) cc_final: 0.8497 (ttp) REVERT: B 556 LYS cc_start: 0.9277 (mmpt) cc_final: 0.8836 (ptmm) REVERT: B 696 VAL cc_start: 0.8575 (t) cc_final: 0.8309 (t) REVERT: B 700 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8732 (mt-10) REVERT: C 425 GLU cc_start: 0.9288 (tt0) cc_final: 0.8859 (tm-30) REVERT: C 426 VAL cc_start: 0.8955 (t) cc_final: 0.8739 (t) REVERT: C 479 MET cc_start: 0.8901 (mtp) cc_final: 0.8678 (mtp) REVERT: C 522 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7180 (mtmt) REVERT: C 535 MET cc_start: 0.8681 (tmm) cc_final: 0.8465 (tmm) REVERT: D 369 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6607 (tt0) REVERT: D 406 LYS cc_start: 0.8990 (mttt) cc_final: 0.8388 (mtpt) REVERT: D 425 GLU cc_start: 0.8276 (tt0) cc_final: 0.7452 (tp30) REVERT: D 441 LEU cc_start: 0.8834 (mt) cc_final: 0.8589 (mt) REVERT: D 447 ILE cc_start: 0.9549 (pt) cc_final: 0.9082 (mp) REVERT: D 479 MET cc_start: 0.9046 (mtt) cc_final: 0.8469 (mtm) REVERT: D 495 ILE cc_start: 0.8979 (mm) cc_final: 0.8748 (mm) REVERT: D 595 ASP cc_start: 0.8086 (t0) cc_final: 0.7859 (t0) REVERT: D 632 ARG cc_start: 0.8246 (ptt180) cc_final: 0.7671 (tpm170) REVERT: E 369 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7438 (mt-10) REVERT: E 432 TYR cc_start: 0.8746 (t80) cc_final: 0.8535 (t80) REVERT: E 456 LEU cc_start: 0.9321 (tp) cc_final: 0.8703 (tp) REVERT: E 459 MET cc_start: 0.9197 (mtp) cc_final: 0.8320 (mtp) REVERT: E 521 MET cc_start: 0.7254 (tmm) cc_final: 0.6778 (tmm) REVERT: E 540 ARG cc_start: 0.8378 (mtt180) cc_final: 0.7958 (mtm-85) REVERT: E 591 VAL cc_start: 0.9630 (t) cc_final: 0.9408 (p) REVERT: E 650 ILE cc_start: 0.8996 (tp) cc_final: 0.8516 (tp) REVERT: E 675 HIS cc_start: 0.7909 (m-70) cc_final: 0.7643 (m90) REVERT: E 678 MET cc_start: 0.8129 (mtm) cc_final: 0.7925 (mtm) REVERT: E 702 HIS cc_start: 0.8671 (m90) cc_final: 0.8196 (m90) REVERT: F 371 GLN cc_start: 0.8731 (tt0) cc_final: 0.8336 (tm-30) REVERT: F 378 VAL cc_start: 0.9010 (t) cc_final: 0.8741 (p) REVERT: F 441 LEU cc_start: 0.8958 (mt) cc_final: 0.8713 (mt) REVERT: F 479 MET cc_start: 0.9101 (mtm) cc_final: 0.8645 (mtm) REVERT: F 480 LEU cc_start: 0.9708 (mt) cc_final: 0.9498 (mt) REVERT: F 496 MET cc_start: 0.8716 (mmm) cc_final: 0.8364 (mmm) REVERT: F 500 LYS cc_start: 0.8402 (pttt) cc_final: 0.7582 (pttm) REVERT: F 503 GLU cc_start: 0.6723 (mp0) cc_final: 0.6458 (mp0) REVERT: F 526 ASN cc_start: 0.7767 (t0) cc_final: 0.6906 (t0) REVERT: F 529 ARG cc_start: 0.8927 (mpt-90) cc_final: 0.8724 (mtm-85) REVERT: F 599 ASP cc_start: 0.8299 (m-30) cc_final: 0.7094 (m-30) REVERT: F 680 TYR cc_start: 0.9074 (t80) cc_final: 0.8496 (t80) outliers start: 1 outliers final: 1 residues processed: 443 average time/residue: 0.1391 time to fit residues: 93.0122 Evaluate side-chains 331 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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: 6.9990 chunk 86 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN C 435 HIS D 419 GLN D 666 GLN F 435 HIS F 617 GLN F 666 GLN F 675 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.073298 restraints weight = 55905.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075050 restraints weight = 36376.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076275 restraints weight = 26267.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077151 restraints weight = 20653.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077697 restraints weight = 17306.918| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19276 Z= 0.163 Angle : 0.740 10.162 26313 Z= 0.356 Chirality : 0.047 0.279 3140 Planarity : 0.005 0.058 3226 Dihedral : 14.149 157.377 2973 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % 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: -1.87 (0.17), residues: 2343 helix: -0.15 (0.17), residues: 923 sheet: -1.01 (0.26), residues: 392 loop : -2.36 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 555 TYR 0.023 0.002 TYR E 432 PHE 0.017 0.002 PHE A 485 TRP 0.014 0.002 TRP B 530 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00371 (19276) covalent geometry : angle 0.74019 (26313) hydrogen bonds : bond 0.03678 ( 729) hydrogen bonds : angle 5.11078 ( 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 447 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.658 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: A 435 HIS cc_start: 0.9021 (t-90) cc_final: 0.8719 (t-90) REVERT: A 521 MET cc_start: 0.7898 (ptp) cc_final: 0.7133 (pmm) REVERT: A 542 MET cc_start: 0.8017 (mmt) cc_final: 0.7714 (mmt) REVERT: A 626 LEU cc_start: 0.9670 (tp) cc_final: 0.9435 (tp) REVERT: A 699 ASP cc_start: 0.9100 (m-30) cc_final: 0.8755 (t70) REVERT: B 419 GLN cc_start: 0.8567 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 445 HIS cc_start: 0.8362 (m-70) cc_final: 0.7816 (m-70) REVERT: B 529 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7874 (mtm-85) REVERT: B 535 MET cc_start: 0.9010 (tmm) cc_final: 0.8771 (tmm) REVERT: B 538 ARG cc_start: 0.7046 (ptp-170) cc_final: 0.6450 (mtm180) REVERT: B 542 MET cc_start: 0.9250 (ttp) cc_final: 0.8802 (ttp) REVERT: B 545 MET cc_start: 0.8003 (mpp) cc_final: 0.7685 (mpp) REVERT: B 556 LYS cc_start: 0.9275 (mmpt) cc_final: 0.8944 (pttp) REVERT: C 425 GLU cc_start: 0.9275 (tt0) cc_final: 0.8830 (tm-30) REVERT: C 426 VAL cc_start: 0.8935 (t) cc_final: 0.8726 (t) REVERT: C 479 MET cc_start: 0.8987 (mtp) cc_final: 0.8691 (mtm) REVERT: C 481 LEU cc_start: 0.8754 (mp) cc_final: 0.8526 (mp) REVERT: C 507 TYR cc_start: 0.8763 (m-10) cc_final: 0.8559 (m-80) REVERT: C 617 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8075 (tp40) REVERT: D 406 LYS cc_start: 0.8971 (mttt) cc_final: 0.8672 (mtpt) REVERT: D 425 GLU cc_start: 0.8174 (tt0) cc_final: 0.7386 (tp30) REVERT: D 426 VAL cc_start: 0.9001 (t) cc_final: 0.8778 (t) REVERT: D 447 ILE cc_start: 0.9524 (pt) cc_final: 0.9057 (mp) REVERT: D 479 MET cc_start: 0.9048 (mtt) cc_final: 0.8785 (mtt) REVERT: D 491 GLU cc_start: 0.7785 (pt0) cc_final: 0.7445 (pt0) REVERT: D 495 ILE cc_start: 0.8874 (mm) cc_final: 0.8643 (mm) REVERT: D 521 MET cc_start: 0.8450 (mpp) cc_final: 0.7618 (mtt) REVERT: D 599 ASP cc_start: 0.8360 (m-30) cc_final: 0.8058 (m-30) REVERT: D 632 ARG cc_start: 0.8236 (ptt180) cc_final: 0.7652 (tpm170) REVERT: E 369 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7315 (mt-10) REVERT: E 456 LEU cc_start: 0.9303 (tp) cc_final: 0.8968 (tp) REVERT: E 459 MET cc_start: 0.9166 (mtp) cc_final: 0.8555 (mtp) REVERT: E 461 HIS cc_start: 0.8521 (m-70) cc_final: 0.8103 (m-70) REVERT: E 517 VAL cc_start: 0.9134 (t) cc_final: 0.8863 (m) REVERT: E 540 ARG cc_start: 0.8406 (mtt180) cc_final: 0.7938 (mtm-85) REVERT: E 555 ARG cc_start: 0.8747 (tmm-80) cc_final: 0.8085 (tmm-80) REVERT: E 650 ILE cc_start: 0.9109 (tp) cc_final: 0.8719 (tp) REVERT: E 670 GLU cc_start: 0.8537 (pm20) cc_final: 0.8326 (pm20) REVERT: E 677 ASP cc_start: 0.7523 (t70) cc_final: 0.7257 (t70) REVERT: E 702 HIS cc_start: 0.8608 (m90) cc_final: 0.8185 (m90) REVERT: F 371 GLN cc_start: 0.8670 (tt0) cc_final: 0.8262 (tm-30) REVERT: F 379 SER cc_start: 0.9045 (p) cc_final: 0.8832 (t) REVERT: F 479 MET cc_start: 0.9032 (mtm) cc_final: 0.8635 (mtm) REVERT: F 480 LEU cc_start: 0.9664 (mt) cc_final: 0.9458 (mt) REVERT: F 496 MET cc_start: 0.8707 (mmm) cc_final: 0.8337 (mmm) REVERT: F 500 LYS cc_start: 0.8383 (pttt) cc_final: 0.7672 (pttm) REVERT: F 503 GLU cc_start: 0.6639 (mp0) cc_final: 0.6344 (mp0) REVERT: F 599 ASP cc_start: 0.8151 (m-30) cc_final: 0.7782 (m-30) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.1336 time to fit residues: 90.8051 Evaluate side-chains 344 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 7.9990 chunk 227 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 692 HIS 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 = 0.3253 r_free = 0.3253 target = 0.086445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.069618 restraints weight = 57042.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.071251 restraints weight = 37190.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.072402 restraints weight = 27259.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.073234 restraints weight = 21634.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073826 restraints weight = 18243.862| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 19276 Z= 0.308 Angle : 0.872 11.445 26313 Z= 0.421 Chirality : 0.050 0.261 3140 Planarity : 0.006 0.054 3226 Dihedral : 14.151 156.834 2973 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % 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: -1.92 (0.17), residues: 2343 helix: -0.31 (0.17), residues: 921 sheet: -1.02 (0.26), residues: 384 loop : -2.26 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 493 TYR 0.026 0.002 TYR E 432 PHE 0.018 0.002 PHE A 368 TRP 0.015 0.002 TRP A 530 HIS 0.008 0.002 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00682 (19276) covalent geometry : angle 0.87242 (26313) hydrogen bonds : bond 0.04399 ( 729) hydrogen bonds : angle 5.49521 ( 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 403 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 0.578 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: 0.9177 (t-90) cc_final: 0.8953 (t-90) REVERT: A 521 MET cc_start: 0.8125 (ptp) cc_final: 0.6412 (pmm) REVERT: A 595 ASP cc_start: 0.6897 (t70) cc_final: 0.6661 (t70) REVERT: A 626 LEU cc_start: 0.9651 (tp) cc_final: 0.9402 (tp) REVERT: A 671 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 699 ASP cc_start: 0.9003 (m-30) cc_final: 0.8698 (t70) REVERT: B 398 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7794 (ptm-80) REVERT: B 419 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 445 HIS cc_start: 0.8450 (m-70) cc_final: 0.7809 (m-70) REVERT: B 479 MET cc_start: 0.9490 (mtm) cc_final: 0.9263 (mtm) REVERT: B 519 THR cc_start: 0.8609 (p) cc_final: 0.8396 (p) REVERT: B 529 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8103 (mtt-85) REVERT: B 535 MET cc_start: 0.9131 (tmm) cc_final: 0.8827 (tmm) REVERT: B 542 MET cc_start: 0.9180 (ttp) cc_final: 0.8540 (ttp) REVERT: B 610 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8511 (pm20) REVERT: C 425 GLU cc_start: 0.9281 (tt0) cc_final: 0.8736 (tm-30) REVERT: C 445 HIS cc_start: 0.8373 (m-70) cc_final: 0.7040 (m170) REVERT: C 480 LEU cc_start: 0.9631 (mt) cc_final: 0.9402 (mt) REVERT: C 481 LEU cc_start: 0.8804 (mp) cc_final: 0.8560 (mp) REVERT: C 507 TYR cc_start: 0.8810 (m-10) cc_final: 0.8550 (m-80) REVERT: D 318 LEU cc_start: 0.8685 (mp) cc_final: 0.8329 (tp) REVERT: D 425 GLU cc_start: 0.8308 (tt0) cc_final: 0.7522 (tp30) REVERT: D 441 LEU cc_start: 0.8669 (mp) cc_final: 0.8240 (mp) REVERT: D 450 ARG cc_start: 0.8661 (mpp80) cc_final: 0.8309 (mpt180) REVERT: D 479 MET cc_start: 0.9068 (mtt) cc_final: 0.8699 (mtm) REVERT: D 491 GLU cc_start: 0.7976 (pt0) cc_final: 0.7603 (pt0) REVERT: D 496 MET cc_start: 0.8399 (mtp) cc_final: 0.8157 (mpp) REVERT: D 632 ARG cc_start: 0.8444 (ptt180) cc_final: 0.7832 (tpm170) REVERT: E 456 LEU cc_start: 0.9347 (tp) cc_final: 0.8973 (tp) REVERT: E 459 MET cc_start: 0.9221 (mtp) cc_final: 0.8525 (mtp) REVERT: E 461 HIS cc_start: 0.8717 (m-70) cc_final: 0.8351 (m-70) REVERT: E 540 ARG cc_start: 0.8449 (mtt180) cc_final: 0.7923 (mtm-85) REVERT: E 555 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8469 (ttp80) REVERT: E 617 GLN cc_start: 0.8711 (tt0) cc_final: 0.8309 (tt0) REVERT: E 677 ASP cc_start: 0.7844 (t70) cc_final: 0.7542 (t70) REVERT: E 702 HIS cc_start: 0.8604 (m90) cc_final: 0.8228 (m90) REVERT: F 371 GLN cc_start: 0.8728 (tt0) cc_final: 0.8380 (tm-30) REVERT: F 378 VAL cc_start: 0.8984 (t) cc_final: 0.8778 (p) REVERT: F 441 LEU cc_start: 0.9064 (mt) cc_final: 0.8747 (mt) REVERT: F 479 MET cc_start: 0.9095 (mtm) cc_final: 0.8726 (mtm) REVERT: F 500 LYS cc_start: 0.8375 (pttt) cc_final: 0.7696 (pttm) REVERT: F 503 GLU cc_start: 0.6710 (mp0) cc_final: 0.6330 (mp0) REVERT: F 597 PHE cc_start: 0.8552 (t80) cc_final: 0.8318 (t80) REVERT: F 599 ASP cc_start: 0.8431 (m-30) cc_final: 0.7614 (m-30) outliers start: 1 outliers final: 0 residues processed: 403 average time/residue: 0.1333 time to fit residues: 82.0830 Evaluate side-chains 320 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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: 5.9990 chunk 54 optimal weight: 2.9990 chunk 220 optimal weight: 0.0980 chunk 223 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN ** A 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN C 435 HIS D 419 GLN E 675 HIS F 435 HIS F 617 GLN F 666 GLN F 675 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.072816 restraints weight = 55788.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.074578 restraints weight = 35947.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.075835 restraints weight = 26061.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.076694 restraints weight = 20440.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077320 restraints weight = 17143.136| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19276 Z= 0.149 Angle : 0.754 10.606 26313 Z= 0.357 Chirality : 0.047 0.191 3140 Planarity : 0.005 0.052 3226 Dihedral : 13.795 161.477 2973 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % 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: -1.46 (0.18), residues: 2343 helix: 0.06 (0.18), residues: 930 sheet: -0.69 (0.27), residues: 398 loop : -2.06 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 422 TYR 0.024 0.002 TYR E 432 PHE 0.018 0.002 PHE D 553 TRP 0.015 0.002 TRP B 530 HIS 0.003 0.001 HIS B 692 Details of bonding type rmsd covalent geometry : bond 0.00346 (19276) covalent geometry : angle 0.75433 (26313) hydrogen bonds : bond 0.03661 ( 729) hydrogen bonds : angle 5.07674 ( 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 425 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 0.693 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 474 VAL cc_start: 0.9229 (t) cc_final: 0.8941 (p) REVERT: A 601 MET cc_start: 0.7528 (tmm) cc_final: 0.7044 (tmm) REVERT: A 626 LEU cc_start: 0.9652 (tp) cc_final: 0.9439 (tp) REVERT: A 699 ASP cc_start: 0.9086 (m-30) cc_final: 0.8739 (t70) REVERT: B 445 HIS cc_start: 0.8328 (m-70) cc_final: 0.7792 (m-70) REVERT: B 479 MET cc_start: 0.9469 (mtm) cc_final: 0.9123 (mtm) REVERT: B 494 LEU cc_start: 0.9114 (pt) cc_final: 0.8840 (pp) REVERT: B 529 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7668 (mtt180) REVERT: B 535 MET cc_start: 0.9106 (tmm) cc_final: 0.8837 (tmm) REVERT: B 542 MET cc_start: 0.9153 (ttp) cc_final: 0.8247 (ttp) REVERT: B 556 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8910 (pttp) REVERT: C 425 GLU cc_start: 0.9268 (tt0) cc_final: 0.8850 (tm-30) REVERT: C 426 VAL cc_start: 0.9000 (t) cc_final: 0.8759 (t) REVERT: C 458 LYS cc_start: 0.8238 (mppt) cc_final: 0.8034 (mmtt) REVERT: C 480 LEU cc_start: 0.9619 (mt) cc_final: 0.9389 (mt) REVERT: C 481 LEU cc_start: 0.8763 (mp) cc_final: 0.8490 (mp) REVERT: C 507 TYR cc_start: 0.8800 (m-10) cc_final: 0.8471 (m-80) REVERT: D 318 LEU cc_start: 0.8610 (mp) cc_final: 0.8240 (tp) REVERT: D 425 GLU cc_start: 0.8133 (tt0) cc_final: 0.7376 (tp30) REVERT: D 447 ILE cc_start: 0.9527 (pt) cc_final: 0.9081 (mp) REVERT: D 479 MET cc_start: 0.9021 (mtt) cc_final: 0.8787 (mtm) REVERT: D 491 GLU cc_start: 0.7895 (pt0) cc_final: 0.7520 (pt0) REVERT: D 504 LEU cc_start: 0.8730 (mp) cc_final: 0.8494 (mp) REVERT: D 631 GLN cc_start: 0.8283 (mm110) cc_final: 0.7990 (mm-40) REVERT: D 632 ARG cc_start: 0.8333 (ptt180) cc_final: 0.7718 (tpm170) REVERT: E 456 LEU cc_start: 0.9275 (tp) cc_final: 0.8921 (tp) REVERT: E 459 MET cc_start: 0.9140 (mtp) cc_final: 0.8472 (mtp) REVERT: E 461 HIS cc_start: 0.8516 (m-70) cc_final: 0.8094 (m-70) REVERT: E 500 LYS cc_start: 0.7808 (pptt) cc_final: 0.7367 (tmtt) REVERT: E 540 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7982 (mtm-85) REVERT: E 555 ARG cc_start: 0.8842 (tmm-80) cc_final: 0.8599 (ttp80) REVERT: E 650 ILE cc_start: 0.9141 (tp) cc_final: 0.8745 (tp) REVERT: E 677 ASP cc_start: 0.7934 (t70) cc_final: 0.7633 (t70) REVERT: E 678 MET cc_start: 0.7957 (mtp) cc_final: 0.7681 (mtp) REVERT: E 702 HIS cc_start: 0.8616 (m90) cc_final: 0.8394 (m90) REVERT: F 371 GLN cc_start: 0.8706 (tt0) cc_final: 0.8282 (tm-30) REVERT: F 379 SER cc_start: 0.8971 (p) cc_final: 0.8729 (t) REVERT: F 419 GLN cc_start: 0.8916 (tt0) cc_final: 0.8387 (tm-30) REVERT: F 441 LEU cc_start: 0.8984 (mt) cc_final: 0.8750 (mt) REVERT: F 479 MET cc_start: 0.8978 (mtm) cc_final: 0.8599 (mtm) REVERT: F 480 LEU cc_start: 0.9666 (mm) cc_final: 0.9449 (mt) REVERT: F 496 MET cc_start: 0.8683 (mmm) cc_final: 0.8410 (mmm) REVERT: F 503 GLU cc_start: 0.6852 (mp0) cc_final: 0.6371 (mp0) REVERT: F 599 ASP cc_start: 0.8447 (m-30) cc_final: 0.7541 (m-30) REVERT: F 659 ASP cc_start: 0.7332 (m-30) cc_final: 0.7023 (m-30) outliers start: 1 outliers final: 0 residues processed: 425 average time/residue: 0.1360 time to fit residues: 87.8377 Evaluate side-chains 336 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 4.9990 chunk 173 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 192 optimal weight: 0.0980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN A 631 GLN ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN C 435 HIS D 419 GLN D 666 GLN F 435 HIS F 645 ASN F 666 GLN F 675 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.071032 restraints weight = 56710.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.072752 restraints weight = 36816.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.073945 restraints weight = 26651.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074792 restraints weight = 21029.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075327 restraints weight = 17657.850| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19276 Z= 0.216 Angle : 0.789 11.448 26313 Z= 0.377 Chirality : 0.048 0.310 3140 Planarity : 0.005 0.054 3226 Dihedral : 13.751 173.960 2973 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: -1.41 (0.18), residues: 2343 helix: 0.10 (0.18), residues: 933 sheet: -0.70 (0.27), residues: 387 loop : -2.01 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 390 TYR 0.023 0.002 TYR E 432 PHE 0.015 0.002 PHE A 553 TRP 0.017 0.002 TRP F 530 HIS 0.007 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00490 (19276) covalent geometry : angle 0.78884 (26313) hydrogen bonds : bond 0.03917 ( 729) hydrogen bonds : angle 5.18133 ( 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 401 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.8463 (tpp) cc_final: 0.8256 (tpp) REVERT: A 474 VAL cc_start: 0.9300 (t) cc_final: 0.8958 (p) REVERT: A 699 ASP cc_start: 0.9085 (m-30) cc_final: 0.8764 (t70) REVERT: B 445 HIS cc_start: 0.8393 (m-70) cc_final: 0.7827 (m-70) REVERT: B 529 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.7864 (mtt90) REVERT: B 535 MET cc_start: 0.9124 (tmm) cc_final: 0.8842 (tmm) REVERT: B 542 MET cc_start: 0.9126 (ttp) cc_final: 0.8537 (ttp) REVERT: C 425 GLU cc_start: 0.9295 (tt0) cc_final: 0.8773 (tm-30) REVERT: C 426 VAL cc_start: 0.9082 (t) cc_final: 0.8781 (t) REVERT: C 458 LYS cc_start: 0.8376 (mppt) cc_final: 0.8062 (mmtt) REVERT: C 480 LEU cc_start: 0.9600 (mt) cc_final: 0.9370 (mt) REVERT: C 481 LEU cc_start: 0.8776 (mp) cc_final: 0.8500 (mp) REVERT: C 507 TYR cc_start: 0.8763 (m-10) cc_final: 0.8463 (m-80) REVERT: C 521 MET cc_start: 0.6669 (mmp) cc_final: 0.5801 (mmp) REVERT: C 553 PHE cc_start: 0.8961 (t80) cc_final: 0.8692 (t80) REVERT: D 318 LEU cc_start: 0.8640 (mp) cc_final: 0.8289 (tp) REVERT: D 425 GLU cc_start: 0.8188 (tt0) cc_final: 0.7401 (tp30) REVERT: D 426 VAL cc_start: 0.9056 (t) cc_final: 0.8843 (t) REVERT: D 441 LEU cc_start: 0.8497 (mp) cc_final: 0.8082 (mt) REVERT: D 447 ILE cc_start: 0.9576 (pt) cc_final: 0.9154 (mp) REVERT: D 479 MET cc_start: 0.9095 (mtt) cc_final: 0.8589 (mtt) REVERT: D 491 GLU cc_start: 0.7925 (pt0) cc_final: 0.7575 (pt0) REVERT: D 631 GLN cc_start: 0.8237 (mm110) cc_final: 0.7865 (mm-40) REVERT: D 632 ARG cc_start: 0.8437 (ptt180) cc_final: 0.7788 (tpm170) REVERT: E 456 LEU cc_start: 0.9304 (tp) cc_final: 0.8922 (tp) REVERT: E 459 MET cc_start: 0.9218 (mtp) cc_final: 0.8458 (mtp) REVERT: E 461 HIS cc_start: 0.8573 (m-70) cc_final: 0.8242 (m-70) REVERT: E 521 MET cc_start: 0.7218 (tmm) cc_final: 0.6297 (tmm) REVERT: E 540 ARG cc_start: 0.8491 (mtt180) cc_final: 0.7654 (tmm-80) REVERT: E 555 ARG cc_start: 0.8895 (tmm-80) cc_final: 0.8656 (ttp80) REVERT: E 628 LEU cc_start: 0.9346 (mt) cc_final: 0.9141 (mt) REVERT: E 678 MET cc_start: 0.7969 (mtp) cc_final: 0.7565 (mtp) REVERT: E 702 HIS cc_start: 0.8647 (m90) cc_final: 0.8384 (m90) REVERT: F 371 GLN cc_start: 0.8660 (tt0) cc_final: 0.8355 (tm-30) REVERT: F 379 SER cc_start: 0.8963 (p) cc_final: 0.8732 (t) REVERT: F 419 GLN cc_start: 0.8950 (tt0) cc_final: 0.8432 (tm-30) REVERT: F 441 LEU cc_start: 0.9034 (mt) cc_final: 0.8825 (mt) REVERT: F 479 MET cc_start: 0.9028 (mtm) cc_final: 0.8660 (mtm) REVERT: F 496 MET cc_start: 0.8713 (mmm) cc_final: 0.8401 (mmm) REVERT: F 503 GLU cc_start: 0.6820 (mp0) cc_final: 0.6222 (mp0) REVERT: F 599 ASP cc_start: 0.8448 (m-30) cc_final: 0.7497 (m-30) REVERT: F 632 ARG cc_start: 0.8490 (ptm-80) cc_final: 0.8260 (ptm-80) REVERT: F 641 LEU cc_start: 0.8964 (mp) cc_final: 0.8609 (mm) REVERT: F 680 TYR cc_start: 0.9204 (t80) cc_final: 0.8533 (t80) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1290 time to fit residues: 80.1981 Evaluate side-chains 330 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 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: 0.7980 chunk 1 optimal weight: 8.9990 chunk 181 optimal weight: 0.3980 chunk 185 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN A 671 GLN B 617 GLN B 645 ASN B 671 GLN C 435 HIS D 419 GLN E 415 ASN E 675 HIS F 435 HIS F 645 ASN F 675 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.075155 restraints weight = 55227.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076919 restraints weight = 35838.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078188 restraints weight = 26013.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079084 restraints weight = 20351.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079709 restraints weight = 16996.811| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19276 Z= 0.133 Angle : 0.748 12.694 26313 Z= 0.354 Chirality : 0.047 0.282 3140 Planarity : 0.005 0.051 3226 Dihedral : 13.480 176.949 2973 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.05 % Allowed : 1.50 % Favored : 98.45 % 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: -1.13 (0.18), residues: 2343 helix: 0.41 (0.18), residues: 927 sheet: -0.59 (0.27), residues: 380 loop : -1.89 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 632 TYR 0.011 0.001 TYR A 432 PHE 0.016 0.002 PHE A 423 TRP 0.019 0.002 TRP B 530 HIS 0.011 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00303 (19276) covalent geometry : angle 0.74834 (26313) hydrogen bonds : bond 0.03394 ( 729) hydrogen bonds : angle 4.86700 ( 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 445 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 0.859 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: 0.9044 (t-90) cc_final: 0.8804 (t-90) REVERT: A 472 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8535 (mttt) REVERT: A 521 MET cc_start: 0.8381 (ptp) cc_final: 0.7960 (ptp) REVERT: A 675 HIS cc_start: 0.7499 (m170) cc_final: 0.7227 (m-70) REVERT: A 699 ASP cc_start: 0.9090 (m-30) cc_final: 0.8751 (t70) REVERT: B 477 ASN cc_start: 0.8836 (m-40) cc_final: 0.8595 (m-40) REVERT: B 529 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.8000 (mtt-85) REVERT: B 535 MET cc_start: 0.9056 (tmm) cc_final: 0.8830 (tmm) REVERT: B 542 MET cc_start: 0.9109 (ttp) cc_final: 0.8520 (ttp) REVERT: B 556 LYS cc_start: 0.9221 (mmpt) cc_final: 0.8938 (pttp) REVERT: C 425 GLU cc_start: 0.9286 (tt0) cc_final: 0.8856 (tm-30) REVERT: C 458 LYS cc_start: 0.8246 (mppt) cc_final: 0.8002 (mmtt) REVERT: C 481 LEU cc_start: 0.8815 (mp) cc_final: 0.8506 (mp) REVERT: C 507 TYR cc_start: 0.8667 (m-10) cc_final: 0.8383 (m-80) REVERT: C 521 MET cc_start: 0.6480 (mmp) cc_final: 0.5534 (mmp) REVERT: D 318 LEU cc_start: 0.8564 (mp) cc_final: 0.8249 (tp) REVERT: D 425 GLU cc_start: 0.8058 (tt0) cc_final: 0.7349 (tp30) REVERT: D 447 ILE cc_start: 0.9556 (pt) cc_final: 0.9037 (mp) REVERT: D 491 GLU cc_start: 0.7908 (pt0) cc_final: 0.7522 (pt0) REVERT: D 631 GLN cc_start: 0.8348 (mm110) cc_final: 0.8008 (mm-40) REVERT: D 632 ARG cc_start: 0.8249 (ptt180) cc_final: 0.7613 (tpm170) REVERT: E 369 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7188 (mt-10) REVERT: E 456 LEU cc_start: 0.9254 (tp) cc_final: 0.8832 (tp) REVERT: E 459 MET cc_start: 0.9196 (mtp) cc_final: 0.8264 (mtp) REVERT: E 461 HIS cc_start: 0.8322 (m-70) cc_final: 0.7910 (m-70) REVERT: E 521 MET cc_start: 0.7242 (tmm) cc_final: 0.6744 (tmm) REVERT: E 526 ASN cc_start: 0.8508 (m-40) cc_final: 0.8254 (m-40) REVERT: E 540 ARG cc_start: 0.8493 (mtt180) cc_final: 0.7988 (mtm-85) REVERT: E 650 ILE cc_start: 0.9202 (tp) cc_final: 0.8779 (tp) REVERT: E 678 MET cc_start: 0.7797 (mtp) cc_final: 0.7564 (mtp) REVERT: E 702 HIS cc_start: 0.8563 (m90) cc_final: 0.8350 (m90) REVERT: F 371 GLN cc_start: 0.8615 (tt0) cc_final: 0.8241 (tm-30) REVERT: F 379 SER cc_start: 0.8913 (p) cc_final: 0.8694 (t) REVERT: F 419 GLN cc_start: 0.8889 (tt0) cc_final: 0.8631 (tm-30) REVERT: F 479 MET cc_start: 0.8978 (mtm) cc_final: 0.8503 (mtm) REVERT: F 496 MET cc_start: 0.8646 (mmm) cc_final: 0.8348 (mmm) REVERT: F 503 GLU cc_start: 0.6690 (mp0) cc_final: 0.6360 (mp0) REVERT: F 510 ILE cc_start: 0.9183 (pt) cc_final: 0.8863 (mt) REVERT: F 599 ASP cc_start: 0.8473 (m-30) cc_final: 0.7559 (m-30) REVERT: F 641 LEU cc_start: 0.8967 (mp) cc_final: 0.8441 (mp) REVERT: F 645 ASN cc_start: 0.9173 (m-40) cc_final: 0.8947 (m-40) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.1345 time to fit residues: 91.4476 Evaluate side-chains 344 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS D 419 GLN D 645 ASN D 666 GLN F 617 GLN F 645 ASN F 675 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.071841 restraints weight = 56476.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073575 restraints weight = 36413.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074814 restraints weight = 26476.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075661 restraints weight = 20811.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076291 restraints weight = 17496.410| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4617 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= 0.202 Angle : 0.796 11.522 26313 Z= 0.381 Chirality : 0.049 0.284 3140 Planarity : 0.005 0.072 3226 Dihedral : 13.427 174.952 2973 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -1.18 (0.18), residues: 2343 helix: 0.28 (0.18), residues: 926 sheet: -0.53 (0.27), residues: 367 loop : -1.86 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 390 TYR 0.021 0.002 TYR F 432 PHE 0.028 0.002 PHE B 423 TRP 0.022 0.002 TRP F 530 HIS 0.009 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00463 (19276) covalent geometry : angle 0.79640 (26313) hydrogen bonds : bond 0.03881 ( 729) hydrogen bonds : angle 5.07906 ( 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 392 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.685 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: 0.9167 (t-90) cc_final: 0.8756 (t-90) REVERT: A 472 LYS cc_start: 0.9061 (mtmt) cc_final: 0.7566 (mttt) REVERT: A 481 LEU cc_start: 0.9677 (mm) cc_final: 0.9448 (mm) REVERT: A 521 MET cc_start: 0.8232 (ptp) cc_final: 0.8024 (ptp) REVERT: A 675 HIS cc_start: 0.7576 (m170) cc_final: 0.7312 (m-70) REVERT: A 699 ASP cc_start: 0.9142 (m-30) cc_final: 0.8769 (t70) REVERT: B 445 HIS cc_start: 0.8303 (m-70) cc_final: 0.7980 (m-70) REVERT: B 529 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7528 (mtt180) REVERT: B 535 MET cc_start: 0.9076 (tmm) cc_final: 0.8849 (tmm) REVERT: B 542 MET cc_start: 0.9073 (ttp) cc_final: 0.8456 (ttp) REVERT: B 642 ILE cc_start: 0.8426 (mm) cc_final: 0.8164 (tp) REVERT: C 425 GLU cc_start: 0.9322 (tt0) cc_final: 0.8730 (tm-30) REVERT: C 445 HIS cc_start: 0.8315 (m-70) cc_final: 0.7167 (m170) REVERT: C 481 LEU cc_start: 0.8797 (mp) cc_final: 0.8506 (mp) REVERT: C 507 TYR cc_start: 0.8736 (m-10) cc_final: 0.8405 (m-80) REVERT: C 522 LYS cc_start: 0.8309 (mmpt) cc_final: 0.7342 (mtmt) REVERT: D 318 LEU cc_start: 0.8634 (mp) cc_final: 0.8316 (tp) REVERT: D 425 GLU cc_start: 0.8249 (tt0) cc_final: 0.7510 (tp30) REVERT: D 447 ILE cc_start: 0.9564 (pt) cc_final: 0.9066 (mp) REVERT: D 479 MET cc_start: 0.8795 (mtm) cc_final: 0.8356 (mtm) REVERT: D 491 GLU cc_start: 0.7941 (pt0) cc_final: 0.7618 (pt0) REVERT: D 631 GLN cc_start: 0.8339 (mm110) cc_final: 0.7940 (mm-40) REVERT: D 632 ARG cc_start: 0.8387 (ptt180) cc_final: 0.7716 (tpm170) REVERT: E 329 LYS cc_start: 0.7996 (mmpt) cc_final: 0.6605 (tptt) REVERT: E 456 LEU cc_start: 0.9301 (tp) cc_final: 0.8986 (tp) REVERT: E 459 MET cc_start: 0.9148 (mtp) cc_final: 0.8422 (mtp) REVERT: E 461 HIS cc_start: 0.8547 (m-70) cc_final: 0.8195 (m-70) REVERT: E 540 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7994 (mtm-85) REVERT: E 618 LYS cc_start: 0.8587 (mttt) cc_final: 0.7902 (mmtt) REVERT: E 670 GLU cc_start: 0.8370 (pm20) cc_final: 0.8079 (pm20) REVERT: E 678 MET cc_start: 0.7874 (mtp) cc_final: 0.7472 (mtp) REVERT: F 371 GLN cc_start: 0.8685 (tt0) cc_final: 0.8303 (tm-30) REVERT: F 419 GLN cc_start: 0.8991 (tt0) cc_final: 0.8537 (tm-30) REVERT: F 464 VAL cc_start: 0.9133 (t) cc_final: 0.8912 (m) REVERT: F 496 MET cc_start: 0.8717 (mmm) cc_final: 0.8410 (mmm) REVERT: F 503 GLU cc_start: 0.6833 (mp0) cc_final: 0.6446 (mp0) REVERT: F 599 ASP cc_start: 0.8555 (m-30) cc_final: 0.7560 (m-30) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1244 time to fit residues: 76.2304 Evaluate side-chains 329 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 4.9990 chunk 142 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 224 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 144 optimal weight: 0.0670 chunk 129 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN C 435 HIS C 675 HIS D 419 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 HIS F 617 GLN F 675 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076329 restraints weight = 55703.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077875 restraints weight = 35527.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079831 restraints weight = 24398.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.079997 restraints weight = 18251.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080095 restraints weight = 16371.180| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19276 Z= 0.128 Angle : 0.761 11.122 26313 Z= 0.360 Chirality : 0.048 0.273 3140 Planarity : 0.005 0.064 3226 Dihedral : 13.220 166.801 2973 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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: -1.02 (0.18), residues: 2343 helix: 0.39 (0.18), residues: 931 sheet: -0.38 (0.28), residues: 367 loop : -1.77 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 661 TYR 0.018 0.002 TYR F 680 PHE 0.024 0.002 PHE C 652 TRP 0.022 0.001 TRP B 530 HIS 0.003 0.001 HIS E 625 Details of bonding type rmsd covalent geometry : bond 0.00296 (19276) covalent geometry : angle 0.76122 (26313) hydrogen bonds : bond 0.03476 ( 729) hydrogen bonds : angle 4.86450 ( 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 428 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.8949 (t-90) cc_final: 0.8608 (t-90) REVERT: A 472 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8543 (mttt) REVERT: A 601 MET cc_start: 0.7706 (tmm) cc_final: 0.7146 (tmm) REVERT: A 675 HIS cc_start: 0.7514 (m170) cc_final: 0.7287 (m-70) REVERT: A 699 ASP cc_start: 0.9049 (m-30) cc_final: 0.8708 (t70) REVERT: B 445 HIS cc_start: 0.8119 (m-70) cc_final: 0.7853 (m-70) REVERT: B 529 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7521 (mtm180) REVERT: B 535 MET cc_start: 0.9024 (tmm) cc_final: 0.8807 (tmm) REVERT: B 542 MET cc_start: 0.9052 (ttp) cc_final: 0.8412 (ttp) REVERT: B 556 LYS cc_start: 0.9250 (mmpt) cc_final: 0.8910 (pttp) REVERT: B 642 ILE cc_start: 0.8348 (mm) cc_final: 0.8076 (tp) REVERT: C 425 GLU cc_start: 0.9317 (tt0) cc_final: 0.8854 (tm-30) REVERT: C 481 LEU cc_start: 0.8824 (mp) cc_final: 0.8536 (mp) REVERT: C 496 MET cc_start: 0.8060 (ppp) cc_final: 0.7679 (ppp) REVERT: C 500 LYS cc_start: 0.8502 (pptt) cc_final: 0.8156 (ptpt) REVERT: C 507 TYR cc_start: 0.8660 (m-10) cc_final: 0.8390 (m-80) REVERT: C 522 LYS cc_start: 0.8337 (mmpt) cc_final: 0.7396 (mtmt) REVERT: C 617 GLN cc_start: 0.8247 (tp40) cc_final: 0.7839 (tp40) REVERT: D 318 LEU cc_start: 0.8620 (mp) cc_final: 0.8314 (tp) REVERT: D 369 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7254 (mt-10) REVERT: D 447 ILE cc_start: 0.9517 (pt) cc_final: 0.8952 (mt) REVERT: D 479 MET cc_start: 0.8608 (mtm) cc_final: 0.8257 (mtm) REVERT: D 481 LEU cc_start: 0.9522 (mp) cc_final: 0.9257 (mp) REVERT: D 521 MET cc_start: 0.8475 (mpp) cc_final: 0.7732 (mtt) REVERT: D 631 GLN cc_start: 0.8241 (mm110) cc_final: 0.7898 (mm-40) REVERT: D 632 ARG cc_start: 0.8242 (ptt180) cc_final: 0.7596 (tpm170) REVERT: E 369 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7184 (mt-10) REVERT: E 459 MET cc_start: 0.9048 (mtp) cc_final: 0.8395 (mtp) REVERT: E 461 HIS cc_start: 0.8313 (m-70) cc_final: 0.7953 (m-70) REVERT: E 521 MET cc_start: 0.7005 (tmm) cc_final: 0.6656 (tmm) REVERT: E 535 MET cc_start: 0.9300 (ttp) cc_final: 0.7969 (tmm) REVERT: E 540 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7967 (mtm-85) REVERT: E 617 GLN cc_start: 0.8596 (tt0) cc_final: 0.8343 (tt0) REVERT: E 650 ILE cc_start: 0.9218 (tp) cc_final: 0.8650 (tp) REVERT: E 678 MET cc_start: 0.7775 (mtp) cc_final: 0.7565 (mtp) REVERT: F 371 GLN cc_start: 0.8551 (tt0) cc_final: 0.8192 (tm-30) REVERT: F 379 SER cc_start: 0.8950 (p) cc_final: 0.8692 (t) REVERT: F 419 GLN cc_start: 0.8893 (tt0) cc_final: 0.8655 (tm-30) REVERT: F 496 MET cc_start: 0.8691 (mmm) cc_final: 0.8462 (mmm) REVERT: F 503 GLU cc_start: 0.6822 (mp0) cc_final: 0.6424 (mp0) REVERT: F 510 ILE cc_start: 0.9176 (pt) cc_final: 0.8843 (mt) REVERT: F 599 ASP cc_start: 0.8413 (m-30) cc_final: 0.7307 (m-30) REVERT: F 641 LEU cc_start: 0.8948 (mp) cc_final: 0.8234 (mp) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.1242 time to fit residues: 82.9067 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 : 0.743 ------------------------------------------------------------------------------- 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: 3.9990 chunk 203 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 89 optimal weight: 0.0470 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 overall best weight: 2.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 ASN B 692 HIS C 653 GLN D 645 ASN E 512 HIS E 617 GLN E 666 GLN F 617 GLN F 675 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.073147 restraints weight = 56553.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074905 restraints weight = 36848.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076105 restraints weight = 26699.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076980 restraints weight = 21058.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077598 restraints weight = 17640.176| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19276 Z= 0.179 Angle : 0.787 11.639 26313 Z= 0.375 Chirality : 0.049 0.305 3140 Planarity : 0.005 0.063 3226 Dihedral : 13.213 161.044 2973 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.09 (0.18), residues: 2343 helix: 0.36 (0.18), residues: 922 sheet: -0.49 (0.27), residues: 374 loop : -1.80 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 661 TYR 0.017 0.002 TYR C 331 PHE 0.019 0.002 PHE B 423 TRP 0.019 0.002 TRP B 530 HIS 0.008 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00415 (19276) covalent geometry : angle 0.78713 (26313) hydrogen bonds : bond 0.03733 ( 729) hydrogen bonds : angle 5.00051 ( 2068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.47 seconds wall clock time: 49 minutes 20.93 seconds (2960.93 seconds total)