Starting phenix.real_space_refine on Sat Sep 12 21:58:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8o_10402/09_2026/6t8o_10402.map" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 90 5.16 5 C 11846 2.51 5 N 3249 2.21 5 O 3583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18806 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3014 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 368} Chain breaks: 1 Chain: "B" 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: "C" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3038 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 371} Chain breaks: 1 Chain: "D" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3018 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 369} Chain breaks: 1 Chain: "E" 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: "F" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3029 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 1 Chain: "G" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} 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: 3.55, per 1000 atoms: 0.19 Number of scatterers: 18806 At special positions: 0 Unit cell: (140.432, 103.752, 132.048, 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 38 15.00 O 3583 8.00 N 3249 7.00 C 11846 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: 1.07 Conformation dependent library (CDL) restraints added in 529.0 milliseconds 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 43.3% alpha, 13.8% beta 13 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.778A pdb=" N MET A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 removed outlier: 3.964A pdb=" N ILE A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.009A pdb=" N ILE A 506 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 507 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 546 Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.532A pdb=" N PHE A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 604 removed outlier: 3.902A pdb=" N MET A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 697 through 710 Processing helix chain 'A' and resid 717 through 721 removed outlier: 3.593A pdb=" N ILE A 720 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 721 " --> pdb=" O GLU A 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 721' Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.794A pdb=" N LEU B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 321 " --> pdb=" O LEU B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 321' Processing helix chain 'B' and resid 332 through 350 removed outlier: 4.059A 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 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 471 through 487 removed outlier: 4.134A pdb=" N LYS B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 removed outlier: 3.692A pdb=" N SER B 505 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 506 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 507 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 546 Processing helix chain 'B' and resid 549 through 563 removed outlier: 3.688A pdb=" N PHE B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 604 removed outlier: 3.624A pdb=" N MET B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 619 removed outlier: 3.640A pdb=" N GLU B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 646 removed outlier: 4.643A pdb=" N ASN B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 663 removed outlier: 3.511A pdb=" N THR B 662 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 710 Processing helix chain 'C' and resid 332 through 349 Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 422 through 428 Processing helix chain 'C' and resid 429 through 434 removed outlier: 4.122A pdb=" N GLU C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 503 through 508 removed outlier: 3.634A pdb=" N ILE C 506 " --> pdb=" O GLU C 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 546 Processing helix chain 'C' and resid 549 through 563 Processing helix chain 'C' and resid 596 through 604 removed outlier: 3.856A pdb=" N MET C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 619 removed outlier: 3.703A pdb=" N GLU C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS C 618 " --> pdb=" O ARG C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 646 removed outlier: 4.254A pdb=" N ASN C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 641 through 646' Processing helix chain 'C' and resid 656 through 664 Processing helix chain 'C' and resid 668 through 672 removed outlier: 3.699A pdb=" N GLN C 671 " --> pdb=" O GLY C 668 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 672 " --> pdb=" O ALA C 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 668 through 672' Processing helix chain 'C' and resid 697 through 710 Processing helix chain 'C' and resid 717 through 721 removed outlier: 3.751A pdb=" N ILE C 720 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.726A pdb=" N LEU D 321 " --> pdb=" O LEU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 350 removed outlier: 3.881A pdb=" N PHE D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 383 Processing helix chain 'D' and resid 384 through 392 removed outlier: 3.562A pdb=" N LEU D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 428 Processing helix chain 'D' and resid 429 through 434 removed outlier: 3.610A pdb=" N ASP D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.628A pdb=" N TYR D 507 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 546 Processing helix chain 'D' and resid 549 through 563 removed outlier: 3.557A pdb=" N GLU D 561 " --> pdb=" O VAL D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 604 removed outlier: 3.604A pdb=" N MET D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 617 removed outlier: 3.817A pdb=" N GLU D 609 " --> pdb=" O GLY D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 646 removed outlier: 3.836A pdb=" N ASN D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'D' and resid 668 through 672 removed outlier: 3.607A pdb=" N GLN D 671 " --> pdb=" O GLY D 668 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 672 " --> pdb=" O ALA D 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 668 through 672' Processing helix chain 'D' and resid 697 through 712 removed outlier: 3.703A pdb=" N ARG D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 721 removed outlier: 3.526A pdb=" N ILE D 720 " --> pdb=" O ILE D 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 321 removed outlier: 3.588A pdb=" N LEU E 320 " --> pdb=" O PRO E 317 " (cutoff:3.500A) removed outlier: 3.835A 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 391 Processing helix chain 'E' and resid 422 through 428 Processing helix chain 'E' and resid 429 through 434 removed outlier: 3.576A pdb=" N ASP E 433 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 520 through 546 Processing helix chain 'E' and resid 549 through 563 Processing helix chain 'E' and resid 596 through 604 removed outlier: 3.734A pdb=" N MET E 600 " --> pdb=" O GLU E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 619 removed outlier: 3.899A pdb=" N GLU E 609 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS E 618 " --> pdb=" O ARG E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 644 Processing helix chain 'E' and resid 656 through 664 Processing helix chain 'E' and resid 668 through 672 removed outlier: 3.777A pdb=" N LEU E 672 " --> pdb=" O ALA E 669 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 710 removed outlier: 3.520A pdb=" N VAL E 701 " --> pdb=" O SER E 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 removed outlier: 3.587A pdb=" N LEU F 320 " --> pdb=" O PRO F 317 " (cutoff:3.500A) removed outlier: 3.553A 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 350 Processing helix chain 'F' and resid 378 through 383 Processing helix chain 'F' and resid 384 through 392 Processing helix chain 'F' and resid 422 through 428 Processing helix chain 'F' and resid 429 through 434 Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.823A pdb=" N ILE F 506 " --> pdb=" O GLU F 503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR F 507 " --> pdb=" O LEU F 504 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 508 " --> pdb=" O SER F 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 520 through 546 Processing helix chain 'F' and resid 549 through 563 Processing helix chain 'F' and resid 596 through 605 Processing helix chain 'F' and resid 605 through 619 removed outlier: 4.026A pdb=" N GLU F 609 " --> pdb=" O GLY F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 646 removed outlier: 3.921A pdb=" N ASN F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 665 Processing helix chain 'F' and resid 697 through 712 Processing helix chain 'F' and resid 717 through 721 removed outlier: 3.731A pdb=" N ILE F 720 " --> pdb=" O ILE F 717 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU F 721 " --> pdb=" O GLU F 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 717 through 721' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 360 removed outlier: 6.971A pdb=" N GLU A 369 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL A 359 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG A 367 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 445 removed outlier: 5.261A pdb=" N ALA A 442 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 454 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.543A pdb=" N VAL A 591 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 495 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 590 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 627 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 592 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA A 629 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 594 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 463 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 649 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 651 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 356 through 360 Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 445 removed outlier: 5.298A pdb=" N ALA B 442 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR B 454 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY B 444 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 492 through 497 removed outlier: 3.669A pdb=" N VAL B 591 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 590 " --> pdb=" O HIS B 625 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 627 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B 592 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 629 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL B 594 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE B 650 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU B 463 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA B 651 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU B 679 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 361 removed outlier: 5.383A pdb=" N VAL C 356 " --> pdb=" O GLN C 371 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLN C 371 " --> pdb=" O VAL C 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 440 through 445 removed outlier: 5.365A pdb=" N ALA C 442 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR C 454 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY C 444 " --> pdb=" O ILE C 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 492 through 495 removed outlier: 6.530A pdb=" N ARG C 493 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL C 593 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 495 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU C 463 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 651 " --> pdb=" O LEU C 679 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 354 through 361 removed outlier: 5.449A pdb=" N VAL D 356 " --> pdb=" O GLN D 371 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN D 371 " --> pdb=" O VAL D 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 451 through 455 removed outlier: 4.037A pdb=" N GLY D 444 " --> pdb=" O ILE D 452 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR D 454 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA D 442 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 445 " --> pdb=" O HIS D 692 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 649 " --> pdb=" O LEU D 681 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 462 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG D 493 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL D 593 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE D 495 " --> pdb=" O VAL D 593 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 354 through 360 removed outlier: 5.590A pdb=" N VAL E 356 " --> pdb=" O GLN E 371 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN E 371 " --> pdb=" O VAL E 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 440 through 445 removed outlier: 5.097A pdb=" N ALA E 442 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR E 454 " --> pdb=" O ALA E 442 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY E 444 " --> pdb=" O ILE E 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.056A pdb=" N LEU E 462 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE E 650 " --> pdb=" O HIS E 461 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU E 463 " --> pdb=" O ILE E 650 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 649 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 354 through 360 removed outlier: 5.886A pdb=" N VAL F 356 " --> pdb=" O GLN F 371 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN F 371 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 451 through 455 removed outlier: 3.603A pdb=" N GLY F 444 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR F 454 " --> pdb=" O ALA F 442 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA F 442 " --> pdb=" O THR F 454 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS F 445 " --> pdb=" O HIS F 692 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE F 650 " --> pdb=" O HIS F 461 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU F 463 " --> pdb=" O ILE F 650 " (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5388 1.33 - 1.45: 2468 1.45 - 1.57: 11092 1.57 - 1.69: 68 1.69 - 1.81: 174 Bond restraints: 19190 Sorted by residual: bond pdb=" C3' DT H 11 " pdb=" O3' DT H 11 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" C1' DT H 7 " pdb=" N1 DT H 7 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.81e+00 bond pdb=" C1' DT G 10 " pdb=" N1 DT G 10 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.36e+00 bond pdb=" C SER A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.28e-02 6.10e+03 5.03e+00 bond pdb=" C LEU E 514 " pdb=" N CYS E 515 " ideal model delta sigma weight residual 1.339 1.217 0.122 5.57e-02 3.22e+02 4.80e+00 ... (remaining 19185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 25570 2.56 - 5.13: 530 5.13 - 7.69: 42 7.69 - 10.26: 13 10.26 - 12.82: 14 Bond angle restraints: 26169 Sorted by residual: angle pdb=" N VAL F 378 " pdb=" CA VAL F 378 " pdb=" C VAL F 378 " ideal model delta sigma weight residual 113.42 107.55 5.87 1.17e+00 7.31e-01 2.52e+01 angle pdb=" N GLY A 605 " pdb=" CA GLY A 605 " pdb=" C GLY A 605 " ideal model delta sigma weight residual 111.56 116.63 -5.07 1.01e+00 9.80e-01 2.52e+01 angle pdb=" C MET E 459 " pdb=" N PRO E 460 " pdb=" CA PRO E 460 " ideal model delta sigma weight residual 127.00 138.71 -11.71 2.40e+00 1.74e-01 2.38e+01 angle pdb=" C MET D 459 " pdb=" N PRO D 460 " pdb=" CD PRO D 460 " ideal model delta sigma weight residual 120.60 109.99 10.61 2.20e+00 2.07e-01 2.33e+01 angle pdb=" C MET E 459 " pdb=" N PRO E 460 " pdb=" CD PRO E 460 " ideal model delta sigma weight residual 120.60 110.06 10.54 2.20e+00 2.07e-01 2.30e+01 ... (remaining 26164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 11567 32.17 - 64.34: 236 64.34 - 96.52: 3 96.52 - 128.69: 5 128.69 - 160.86: 8 Dihedral angle restraints: 11819 sinusoidal: 4997 harmonic: 6822 Sorted by residual: dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 100.86 -160.86 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 98.36 -158.36 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PA ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 95.75 -155.75 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 11816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2219 0.052 - 0.104: 690 0.104 - 0.156: 188 0.156 - 0.208: 23 0.208 - 0.260: 8 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CB ILE C 395 " pdb=" CA ILE C 395 " pdb=" CG1 ILE C 395 " pdb=" CG2 ILE C 395 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE F 395 " pdb=" CA ILE F 395 " pdb=" CG1 ILE F 395 " pdb=" CG2 ILE F 395 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE B 663 " pdb=" CA ILE B 663 " pdb=" CG1 ILE B 663 " pdb=" CG2 ILE B 663 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3125 not shown) Planarity restraints: 3227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 632 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO E 633 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 633 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 633 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 488 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 489 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 488 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 489 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 489 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 489 " 0.029 5.00e-02 4.00e+02 ... (remaining 3224 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4360 2.80 - 3.32: 16590 3.32 - 3.85: 31122 3.85 - 4.37: 34906 4.37 - 4.90: 60057 Nonbonded interactions: 147035 Sorted by model distance: nonbonded pdb=" O THR B 438 " pdb=" OG SER B 487 " model vdw 2.270 3.040 nonbonded pdb=" O THR A 438 " pdb=" OG SER A 487 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU A 609 " pdb=" OG1 THR A 639 " model vdw 2.277 3.040 nonbonded pdb=" O THR E 438 " pdb=" OG SER E 487 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR F 331 " pdb=" OD1 ASP F 417 " model vdw 2.309 3.040 ... (remaining 147030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 315 through 570 or resid 586 through 801)) selection = chain 'B' selection = (chain 'C' and (resid 315 through 570 or resid 586 through 721 or resid 801)) selection = (chain 'D' and (resid 315 through 570 or resid 586 through 721 or resid 801)) selection = (chain 'E' and (resid 315 through 570 or resid 586 through 801)) selection = (chain 'F' and (resid 315 through 570 or resid 586 through 801)) } ncs_group { reference = (chain 'G' and resid 1 through 12) selection = (chain 'H' and resid 2 through 13) } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.130 Find NCS groups from input model: 0.530 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.006 0.122 19190 Z= 0.270 Angle : 0.924 12.819 26169 Z= 0.510 Chirality : 0.055 0.260 3128 Planarity : 0.007 0.062 3227 Dihedral : 12.693 160.859 7395 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.20 % Allowed : 4.34 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.14), residues: 2350 helix: -2.62 (0.12), residues: 960 sheet: -2.08 (0.23), residues: 399 loop : -2.87 (0.16), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 690 TYR 0.024 0.003 TYR F 507 PHE 0.031 0.003 PHE A 597 TRP 0.030 0.004 TRP A 530 HIS 0.008 0.002 HIS D 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.27 (19190) covalent geometry : angle 0.92366 / 0.51 (26169) hydrogen bonds : bond 0.16342 / 11.38 ( 801) hydrogen bonds : angle 7.06526 / 4.87 ( 2269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 661 time to evaluate : 0.512 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 360 HIS cc_start: 0.7046 (m-70) cc_final: 0.6485 (m170) REVERT: A 369 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6384 (mt-10) REVERT: A 535 MET cc_start: 0.8674 (ttp) cc_final: 0.8409 (ttt) REVERT: A 587 LEU cc_start: 0.8741 (mt) cc_final: 0.8501 (mt) REVERT: A 596 GLU cc_start: 0.7827 (tp30) cc_final: 0.7308 (tp30) REVERT: A 638 ILE cc_start: 0.7808 (mt) cc_final: 0.7599 (pt) REVERT: B 490 SER cc_start: 0.8103 (p) cc_final: 0.7379 (t) REVERT: B 540 ARG cc_start: 0.8073 (mtm180) cc_final: 0.6890 (mtp85) REVERT: B 702 HIS cc_start: 0.8423 (t70) cc_final: 0.8072 (t-170) REVERT: B 706 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8109 (mm-30) REVERT: C 454 THR cc_start: 0.9421 (p) cc_final: 0.9101 (t) REVERT: C 517 VAL cc_start: 0.8725 (t) cc_final: 0.8019 (t) REVERT: C 522 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8125 (mttt) REVERT: C 595 ASP cc_start: 0.7471 (t0) cc_final: 0.7258 (t0) REVERT: C 648 THR cc_start: 0.9380 (m) cc_final: 0.8978 (p) REVERT: C 706 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7031 (pt0) REVERT: D 321 LEU cc_start: 0.8352 (mt) cc_final: 0.8149 (mt) REVERT: D 328 GLN cc_start: 0.6857 (mp10) cc_final: 0.6648 (mp10) REVERT: D 345 ILE cc_start: 0.8864 (mm) cc_final: 0.8597 (mm) REVERT: D 528 LEU cc_start: 0.9370 (mt) cc_final: 0.9140 (mm) REVERT: D 555 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.8195 (ptp-170) REVERT: D 606 LYS cc_start: 0.8261 (tptp) cc_final: 0.7713 (tppp) REVERT: D 609 GLU cc_start: 0.8309 (tt0) cc_final: 0.7964 (tt0) REVERT: D 650 ILE cc_start: 0.9241 (mm) cc_final: 0.8858 (mt) REVERT: D 657 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8022 (ttmt) REVERT: D 662 THR cc_start: 0.8187 (m) cc_final: 0.7961 (p) REVERT: D 666 GLN cc_start: 0.8533 (pt0) cc_final: 0.8265 (pt0) REVERT: D 672 LEU cc_start: 0.9399 (mt) cc_final: 0.9142 (mt) REVERT: D 675 HIS cc_start: 0.6764 (m-70) cc_final: 0.6484 (m-70) REVERT: D 677 ASP cc_start: 0.8344 (t0) cc_final: 0.8130 (t70) REVERT: D 702 HIS cc_start: 0.7739 (m-70) cc_final: 0.7153 (m90) REVERT: D 719 ASP cc_start: 0.7225 (t0) cc_final: 0.6976 (t70) REVERT: D 720 ILE cc_start: 0.8772 (tt) cc_final: 0.8080 (tt) REVERT: E 432 TYR cc_start: 0.9150 (t80) cc_final: 0.8846 (t80) REVERT: E 438 THR cc_start: 0.8816 (p) cc_final: 0.8609 (m) REVERT: E 504 LEU cc_start: 0.8570 (mt) cc_final: 0.8279 (mt) REVERT: E 604 VAL cc_start: 0.7559 (t) cc_final: 0.6975 (t) REVERT: E 611 LEU cc_start: 0.9251 (mt) cc_final: 0.9031 (mt) REVERT: E 617 GLN cc_start: 0.8102 (tt0) cc_final: 0.7806 (tt0) REVERT: F 422 ARG cc_start: 0.7682 (tpp-160) cc_final: 0.7271 (tpp80) REVERT: F 474 VAL cc_start: 0.9089 (t) cc_final: 0.8857 (t) REVERT: F 612 ILE cc_start: 0.9461 (mm) cc_final: 0.9259 (mt) REVERT: F 617 GLN cc_start: 0.7718 (tt0) cc_final: 0.7316 (tt0) REVERT: F 658 ILE cc_start: 0.8093 (mp) cc_final: 0.7816 (mm) outliers start: 4 outliers final: 0 residues processed: 664 average time/residue: 0.1501 time to fit residues: 145.1378 Evaluate side-chains 375 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 30.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN A 435 HIS A 461 HIS A 512 HIS B 645 ASN B 675 HIS C 645 ASN C 666 GLN C 692 HIS C 702 HIS D 383 ASN D 435 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 GLN E 383 ASN E 435 HIS E 445 HIS F 445 HIS F 477 ASN F 549 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095446 restraints weight = 36829.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097832 restraints weight = 23787.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098528 restraints weight = 18053.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100059 restraints weight = 14229.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100061 restraints weight = 12173.623| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19190 Z= 0.174 Angle : 0.745 12.243 26169 Z= 0.368 Chirality : 0.048 0.242 3128 Planarity : 0.006 0.053 3227 Dihedral : 15.270 167.630 2908 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.59 % Allowed : 13.91 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.15), residues: 2350 helix: -0.95 (0.15), residues: 972 sheet: -1.51 (0.24), residues: 373 loop : -2.39 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 614 TYR 0.018 0.002 TYR C 507 PHE 0.017 0.002 PHE F 597 TRP 0.020 0.002 TRP E 530 HIS 0.009 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (19190) covalent geometry : angle 0.74526 / 0.37 (26169) hydrogen bonds : bond 0.04883 / 3.27 ( 801) hydrogen bonds : angle 5.55175 / 3.82 ( 2269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7179 (m-70) cc_final: 0.6751 (m170) REVERT: A 369 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6727 (mt-10) REVERT: A 501 MET cc_start: 0.8362 (mtt) cc_final: 0.8132 (mtm) REVERT: A 638 ILE cc_start: 0.7846 (mt) cc_final: 0.7620 (pt) REVERT: B 383 ASN cc_start: 0.7881 (t0) cc_final: 0.7626 (t0) REVERT: B 398 ARG cc_start: 0.7359 (ttt-90) cc_final: 0.7102 (ttm-80) REVERT: B 479 MET cc_start: 0.8674 (mtt) cc_final: 0.8462 (mtp) REVERT: B 540 ARG cc_start: 0.8066 (mtm180) cc_final: 0.6925 (mtp85) REVERT: B 558 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7729 (pttt) REVERT: C 521 MET cc_start: 0.7797 (mmt) cc_final: 0.6800 (mmt) REVERT: C 648 THR cc_start: 0.9370 (m) cc_final: 0.9136 (p) REVERT: D 555 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8282 (ptp-170) REVERT: D 599 ASP cc_start: 0.7458 (m-30) cc_final: 0.7043 (m-30) REVERT: D 601 MET cc_start: 0.8765 (mtm) cc_final: 0.8531 (mtm) REVERT: D 662 THR cc_start: 0.8281 (m) cc_final: 0.7922 (p) REVERT: D 675 HIS cc_start: 0.6778 (m-70) cc_final: 0.6533 (m-70) REVERT: D 677 ASP cc_start: 0.8661 (t0) cc_final: 0.8336 (t70) REVERT: D 719 ASP cc_start: 0.7132 (t0) cc_final: 0.6829 (t70) REVERT: E 366 THR cc_start: 0.9485 (m) cc_final: 0.9080 (p) REVERT: E 432 TYR cc_start: 0.9120 (t80) cc_final: 0.8880 (t80) REVERT: E 504 LEU cc_start: 0.8604 (mt) cc_final: 0.8398 (mt) REVERT: E 534 GLU cc_start: 0.7899 (tp30) cc_final: 0.7654 (tm-30) REVERT: F 422 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7192 (tpp80) REVERT: F 498 ASP cc_start: 0.8721 (t0) cc_final: 0.8340 (t0) REVERT: F 658 ILE cc_start: 0.8186 (mp) cc_final: 0.7874 (mm) outliers start: 52 outliers final: 21 residues processed: 439 average time/residue: 0.1247 time to fit residues: 86.0003 Evaluate side-chains 360 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 338 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 35 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN A 666 GLN B 631 GLN D 383 ASN D 526 ASN D 645 ASN D 671 GLN E 383 ASN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 HIS F 617 GLN F 702 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096064 restraints weight = 36954.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098148 restraints weight = 25260.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099397 restraints weight = 18409.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100339 restraints weight = 14067.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100406 restraints weight = 12997.412| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19190 Z= 0.136 Angle : 0.688 8.815 26169 Z= 0.336 Chirality : 0.046 0.154 3128 Planarity : 0.005 0.047 3227 Dihedral : 14.940 174.476 2908 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.99 % Allowed : 14.86 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2350 helix: -0.34 (0.16), residues: 983 sheet: -1.12 (0.24), residues: 382 loop : -2.24 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.020 0.002 TYR F 716 PHE 0.016 0.001 PHE F 597 TRP 0.015 0.002 TRP E 530 HIS 0.011 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (19190) covalent geometry : angle 0.68752 / 0.34 (26169) hydrogen bonds : bond 0.04068 / 2.68 ( 801) hydrogen bonds : angle 5.26101 / 3.62 ( 2269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 386 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7178 (m-70) cc_final: 0.6822 (m170) REVERT: A 369 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 624 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8808 (mp) REVERT: A 638 ILE cc_start: 0.7823 (mt) cc_final: 0.7572 (pt) REVERT: B 383 ASN cc_start: 0.7920 (t0) cc_final: 0.7671 (t0) REVERT: B 540 ARG cc_start: 0.7982 (mtm180) cc_final: 0.6874 (mtp85) REVERT: B 558 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7872 (pttp) REVERT: B 678 MET cc_start: 0.4739 (ptp) cc_final: 0.4530 (ptp) REVERT: B 706 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8103 (mm-30) REVERT: C 455 ASP cc_start: 0.8231 (t0) cc_final: 0.7731 (t0) REVERT: C 517 VAL cc_start: 0.9025 (t) cc_final: 0.8809 (m) REVERT: C 521 MET cc_start: 0.7672 (mmt) cc_final: 0.7442 (mmt) REVERT: C 650 ILE cc_start: 0.9353 (mm) cc_final: 0.9058 (mt) REVERT: D 555 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.8227 (ptp-170) REVERT: D 627 ILE cc_start: 0.9498 (mm) cc_final: 0.9251 (mt) REVERT: D 657 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8296 (ttmt) REVERT: D 659 ASP cc_start: 0.7772 (m-30) cc_final: 0.7523 (m-30) REVERT: D 662 THR cc_start: 0.8290 (m) cc_final: 0.7974 (p) REVERT: D 666 GLN cc_start: 0.8479 (pt0) cc_final: 0.8261 (pt0) REVERT: D 675 HIS cc_start: 0.6635 (m-70) cc_final: 0.6386 (m-70) REVERT: D 719 ASP cc_start: 0.7016 (t0) cc_final: 0.6637 (t70) REVERT: E 366 THR cc_start: 0.9461 (m) cc_final: 0.9067 (p) REVERT: F 498 ASP cc_start: 0.8498 (t0) cc_final: 0.8245 (t0) REVERT: F 602 MET cc_start: 0.7768 (tmm) cc_final: 0.7261 (mmp) REVERT: F 658 ILE cc_start: 0.8131 (mp) cc_final: 0.7888 (mm) outliers start: 60 outliers final: 33 residues processed: 420 average time/residue: 0.1216 time to fit residues: 82.3089 Evaluate side-chains 370 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 335 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 44 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN A 625 HIS A 666 GLN B 360 HIS D 383 ASN E 371 GLN E 383 ASN E 445 HIS ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 702 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092002 restraints weight = 37248.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093754 restraints weight = 23751.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094590 restraints weight = 17979.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095873 restraints weight = 14907.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095839 restraints weight = 13538.216| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 19190 Z= 0.267 Angle : 0.771 9.437 26169 Z= 0.376 Chirality : 0.049 0.202 3128 Planarity : 0.005 0.072 3227 Dihedral : 14.848 179.738 2908 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.19 % Allowed : 15.50 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2350 helix: -0.05 (0.16), residues: 977 sheet: -0.99 (0.25), residues: 391 loop : -2.05 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 540 TYR 0.024 0.002 TYR C 507 PHE 0.022 0.002 PHE B 597 TRP 0.014 0.002 TRP D 708 HIS 0.010 0.002 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 (19190) covalent geometry : angle 0.77116 / 0.38 (26169) hydrogen bonds : bond 0.04184 / 2.79 ( 801) hydrogen bonds : angle 5.24460 / 3.61 ( 2269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 341 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8721 (tt) REVERT: A 624 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8878 (mp) REVERT: A 701 VAL cc_start: 0.9242 (t) cc_final: 0.8894 (p) REVERT: B 383 ASN cc_start: 0.8143 (t0) cc_final: 0.7891 (t0) REVERT: B 419 GLN cc_start: 0.7780 (tt0) cc_final: 0.7186 (mt0) REVERT: B 556 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7518 (tttp) REVERT: C 354 VAL cc_start: 0.9002 (p) cc_final: 0.8734 (m) REVERT: C 371 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8760 (tp40) REVERT: C 650 ILE cc_start: 0.9504 (mm) cc_final: 0.9184 (mt) REVERT: D 328 GLN cc_start: 0.6164 (mp10) cc_final: 0.5877 (tm-30) REVERT: D 555 ARG cc_start: 0.8737 (ttp-110) cc_final: 0.8462 (ptp-170) REVERT: D 631 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7759 (mm-40) REVERT: D 657 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8326 (ttmt) REVERT: D 662 THR cc_start: 0.8346 (m) cc_final: 0.8013 (p) REVERT: D 719 ASP cc_start: 0.7145 (t0) cc_final: 0.6877 (t70) REVERT: E 366 THR cc_start: 0.9532 (m) cc_final: 0.9168 (p) REVERT: F 339 MET cc_start: 0.8361 (tpp) cc_final: 0.8027 (tpp) REVERT: F 484 LEU cc_start: 0.9651 (mt) cc_final: 0.9365 (mt) REVERT: F 498 ASP cc_start: 0.8381 (t0) cc_final: 0.8163 (t0) REVERT: F 653 GLN cc_start: 0.8691 (tt0) cc_final: 0.8446 (tt0) REVERT: F 658 ILE cc_start: 0.8237 (mp) cc_final: 0.7978 (mm) outliers start: 84 outliers final: 56 residues processed: 394 average time/residue: 0.1220 time to fit residues: 77.9350 Evaluate side-chains 366 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 308 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 483 ILE Chi-restraints excluded: chain F residue 593 VAL Chi-restraints excluded: chain F residue 601 MET Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 704 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 77 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 233 optimal weight: 0.0010 chunk 27 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS A 666 GLN C 435 HIS C 653 GLN E 371 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096061 restraints weight = 36493.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097227 restraints weight = 24267.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097952 restraints weight = 19461.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098997 restraints weight = 16217.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099030 restraints weight = 14628.172| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19190 Z= 0.138 Angle : 0.673 8.137 26169 Z= 0.325 Chirality : 0.046 0.179 3128 Planarity : 0.004 0.056 3227 Dihedral : 14.586 177.055 2908 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.14 % Allowed : 16.70 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 2350 helix: 0.28 (0.17), residues: 971 sheet: -0.97 (0.25), residues: 388 loop : -1.87 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 555 TYR 0.027 0.002 TYR B 539 PHE 0.019 0.001 PHE D 423 TRP 0.013 0.002 TRP E 530 HIS 0.014 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (19190) covalent geometry : angle 0.67331 / 0.33 (26169) hydrogen bonds : bond 0.03702 / 2.45 ( 801) hydrogen bonds : angle 5.03159 / 3.46 ( 2269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 359 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7634 (m-70) cc_final: 0.6708 (m170) REVERT: A 369 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 445 HIS cc_start: 0.8348 (m-70) cc_final: 0.8078 (m-70) REVERT: A 541 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 607 LYS cc_start: 0.7768 (pptt) cc_final: 0.7482 (ptmt) REVERT: A 624 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8788 (mp) REVERT: A 701 VAL cc_start: 0.9236 (t) cc_final: 0.8882 (p) REVERT: B 383 ASN cc_start: 0.8133 (t0) cc_final: 0.7925 (t0) REVERT: B 419 GLN cc_start: 0.7689 (tt0) cc_final: 0.7097 (mt0) REVERT: C 455 ASP cc_start: 0.8354 (t0) cc_final: 0.7855 (t0) REVERT: C 650 ILE cc_start: 0.9366 (mm) cc_final: 0.9068 (mt) REVERT: C 717 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7358 (mp) REVERT: D 328 GLN cc_start: 0.6015 (mp10) cc_final: 0.5768 (tm-30) REVERT: D 432 TYR cc_start: 0.8873 (t80) cc_final: 0.8547 (t80) REVERT: D 459 MET cc_start: 0.8204 (mmm) cc_final: 0.7876 (mmm) REVERT: D 555 ARG cc_start: 0.8623 (ttp-110) cc_final: 0.8332 (ptp-170) REVERT: D 612 ILE cc_start: 0.9118 (mm) cc_final: 0.8880 (mt) REVERT: D 657 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8226 (ttmt) REVERT: D 662 THR cc_start: 0.8406 (m) cc_final: 0.8038 (p) REVERT: D 719 ASP cc_start: 0.7034 (t0) cc_final: 0.6731 (t70) REVERT: E 366 THR cc_start: 0.9494 (m) cc_final: 0.9086 (p) REVERT: E 548 ARG cc_start: 0.6409 (mmm160) cc_final: 0.6185 (mmm160) REVERT: E 631 GLN cc_start: 0.8506 (mt0) cc_final: 0.8202 (mm-40) REVERT: F 339 MET cc_start: 0.8361 (tpp) cc_final: 0.8158 (tpp) REVERT: F 459 MET cc_start: 0.8459 (mtp) cc_final: 0.8097 (mmm) REVERT: F 484 LEU cc_start: 0.9607 (mt) cc_final: 0.9302 (mt) REVERT: F 658 ILE cc_start: 0.8165 (mp) cc_final: 0.7956 (mm) outliers start: 63 outliers final: 40 residues processed: 397 average time/residue: 0.1199 time to fit residues: 77.1591 Evaluate side-chains 368 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 677 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 75 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN D 671 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.093779 restraints weight = 36767.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095203 restraints weight = 23841.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096178 restraints weight = 18340.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097049 restraints weight = 15123.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097123 restraints weight = 13924.904| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19190 Z= 0.188 Angle : 0.706 10.519 26169 Z= 0.341 Chirality : 0.047 0.193 3128 Planarity : 0.004 0.052 3227 Dihedral : 14.504 178.581 2908 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.04 % Allowed : 16.50 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2350 helix: 0.40 (0.17), residues: 975 sheet: -0.80 (0.25), residues: 393 loop : -1.77 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 555 TYR 0.023 0.002 TYR E 432 PHE 0.028 0.002 PHE E 553 TRP 0.014 0.002 TRP E 530 HIS 0.010 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (19190) covalent geometry : angle 0.70601 / 0.34 (26169) hydrogen bonds : bond 0.03751 / 2.49 ( 801) hydrogen bonds : angle 5.00440 / 3.44 ( 2269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 332 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 541 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8714 (tt) REVERT: A 610 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 624 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8884 (mp) REVERT: A 701 VAL cc_start: 0.9290 (t) cc_final: 0.8980 (p) REVERT: B 383 ASN cc_start: 0.8119 (t0) cc_final: 0.7888 (t0) REVERT: B 419 GLN cc_start: 0.7703 (tt0) cc_final: 0.7123 (mt0) REVERT: B 479 MET cc_start: 0.8649 (mtp) cc_final: 0.8212 (mmt) REVERT: B 540 ARG cc_start: 0.7915 (mtm180) cc_final: 0.6835 (mtp85) REVERT: B 550 LEU cc_start: 0.7998 (mt) cc_final: 0.7769 (mp) REVERT: C 455 ASP cc_start: 0.8403 (t0) cc_final: 0.7949 (t0) REVERT: C 521 MET cc_start: 0.7573 (mmt) cc_final: 0.6472 (mmt) REVERT: C 650 ILE cc_start: 0.9429 (mm) cc_final: 0.9216 (mt) REVERT: C 672 LEU cc_start: 0.9232 (mt) cc_final: 0.8949 (mt) REVERT: C 717 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7392 (mp) REVERT: D 328 GLN cc_start: 0.5995 (mp10) cc_final: 0.5778 (tm-30) REVERT: D 455 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: D 555 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8339 (ptp-170) REVERT: D 612 ILE cc_start: 0.9104 (mm) cc_final: 0.8895 (mt) REVERT: D 657 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8019 (ttmt) REVERT: D 662 THR cc_start: 0.8447 (m) cc_final: 0.8053 (p) REVERT: D 719 ASP cc_start: 0.7032 (t0) cc_final: 0.6743 (t70) REVERT: E 366 THR cc_start: 0.9515 (m) cc_final: 0.9091 (p) REVERT: E 600 MET cc_start: 0.8088 (ttm) cc_final: 0.7804 (mtt) REVERT: F 339 MET cc_start: 0.8345 (tpp) cc_final: 0.8078 (tpp) REVERT: F 484 LEU cc_start: 0.9618 (mt) cc_final: 0.9309 (mt) REVERT: F 602 MET cc_start: 0.7810 (tmm) cc_final: 0.7367 (mmp) REVERT: F 658 ILE cc_start: 0.8251 (mp) cc_final: 0.8045 (mm) outliers start: 81 outliers final: 59 residues processed: 384 average time/residue: 0.1173 time to fit residues: 73.3172 Evaluate side-chains 382 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 675 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 593 VAL Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 677 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 98 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 57 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 227 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN D 371 GLN D 383 ASN D 671 GLN F 419 GLN F 702 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095961 restraints weight = 36553.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098575 restraints weight = 24497.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099235 restraints weight = 17984.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099746 restraints weight = 15161.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100330 restraints weight = 13482.440| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19190 Z= 0.119 Angle : 0.672 11.538 26169 Z= 0.322 Chirality : 0.046 0.237 3128 Planarity : 0.004 0.052 3227 Dihedral : 14.293 179.016 2908 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.39 % Allowed : 17.80 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.17), residues: 2350 helix: 0.59 (0.17), residues: 965 sheet: -0.70 (0.25), residues: 378 loop : -1.62 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 538 TYR 0.023 0.001 TYR B 539 PHE 0.017 0.001 PHE D 423 TRP 0.018 0.001 TRP D 530 HIS 0.011 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (19190) covalent geometry : angle 0.67223 / 0.32 (26169) hydrogen bonds : bond 0.03438 / 2.29 ( 801) hydrogen bonds : angle 4.88285 / 3.36 ( 2269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 363 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 LYS cc_start: 0.7667 (pptt) cc_final: 0.7288 (ptmt) REVERT: A 610 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7924 (tm-30) REVERT: A 624 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 701 VAL cc_start: 0.9211 (t) cc_final: 0.8920 (p) REVERT: B 383 ASN cc_start: 0.8030 (t0) cc_final: 0.7793 (t0) REVERT: B 419 GLN cc_start: 0.7624 (tt0) cc_final: 0.7068 (mt0) REVERT: B 479 MET cc_start: 0.8615 (mtp) cc_final: 0.8363 (tpp) REVERT: B 540 ARG cc_start: 0.7829 (mtm180) cc_final: 0.6754 (mtp85) REVERT: B 587 LEU cc_start: 0.8324 (mm) cc_final: 0.8119 (pt) REVERT: C 455 ASP cc_start: 0.8184 (t0) cc_final: 0.7714 (t0) REVERT: C 650 ILE cc_start: 0.9385 (mm) cc_final: 0.9132 (mt) REVERT: C 672 LEU cc_start: 0.9202 (mt) cc_final: 0.8832 (mt) REVERT: C 717 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7344 (mp) REVERT: D 336 LEU cc_start: 0.8855 (mt) cc_final: 0.8497 (tt) REVERT: D 459 MET cc_start: 0.8171 (mmm) cc_final: 0.7941 (mmm) REVERT: D 547 VAL cc_start: 0.8437 (t) cc_final: 0.8112 (p) REVERT: D 555 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8202 (ptp-170) REVERT: D 618 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8357 (ptmm) REVERT: D 657 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8217 (ttmt) REVERT: D 659 ASP cc_start: 0.7680 (m-30) cc_final: 0.7443 (m-30) REVERT: D 662 THR cc_start: 0.8523 (m) cc_final: 0.8129 (p) REVERT: D 716 TYR cc_start: 0.7847 (m-10) cc_final: 0.7569 (m-10) REVERT: D 719 ASP cc_start: 0.6824 (t0) cc_final: 0.6512 (t70) REVERT: E 366 THR cc_start: 0.9460 (m) cc_final: 0.9044 (p) REVERT: E 628 LEU cc_start: 0.9392 (mt) cc_final: 0.9109 (mt) REVERT: F 439 VAL cc_start: 0.9590 (m) cc_final: 0.9384 (m) REVERT: F 484 LEU cc_start: 0.9588 (mt) cc_final: 0.9281 (mp) REVERT: F 602 MET cc_start: 0.7682 (tmm) cc_final: 0.7366 (mmp) REVERT: F 700 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7411 (mt-10) outliers start: 68 outliers final: 46 residues processed: 406 average time/residue: 0.1196 time to fit residues: 79.4337 Evaluate side-chains 384 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 675 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 677 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN B 625 HIS C 435 HIS D 477 ASN D 671 GLN E 383 ASN F 419 GLN F 702 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092311 restraints weight = 37080.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093775 restraints weight = 23604.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094814 restraints weight = 18173.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095243 restraints weight = 14779.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095396 restraints weight = 13617.632| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 19190 Z= 0.268 Angle : 0.776 11.065 26169 Z= 0.377 Chirality : 0.049 0.228 3128 Planarity : 0.005 0.056 3227 Dihedral : 14.322 177.590 2908 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.09 % Allowed : 18.25 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.17), residues: 2350 helix: 0.54 (0.17), residues: 968 sheet: -0.70 (0.25), residues: 396 loop : -1.59 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 418 TYR 0.022 0.002 TYR D 432 PHE 0.029 0.002 PHE E 553 TRP 0.018 0.002 TRP E 530 HIS 0.010 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 (19190) covalent geometry : angle 0.77556 / 0.38 (26169) hydrogen bonds : bond 0.03940 / 2.61 ( 801) hydrogen bonds : angle 5.05559 / 3.47 ( 2269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 323 time to evaluate : 0.720 Fit side-chains REVERT: A 462 LEU cc_start: 0.8912 (tp) cc_final: 0.8702 (tt) REVERT: A 535 MET cc_start: 0.8721 (tpp) cc_final: 0.8059 (tpp) REVERT: A 610 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 624 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8983 (mp) REVERT: A 701 VAL cc_start: 0.9368 (t) cc_final: 0.9135 (p) REVERT: B 383 ASN cc_start: 0.8202 (t0) cc_final: 0.7986 (t0) REVERT: B 419 GLN cc_start: 0.7791 (tt0) cc_final: 0.7222 (mt0) REVERT: B 479 MET cc_start: 0.8710 (mtp) cc_final: 0.8464 (tpp) REVERT: B 540 ARG cc_start: 0.7891 (mtm180) cc_final: 0.6805 (mtp85) REVERT: C 354 VAL cc_start: 0.9038 (p) cc_final: 0.8766 (m) REVERT: C 521 MET cc_start: 0.7801 (mmt) cc_final: 0.7426 (mmt) REVERT: C 672 LEU cc_start: 0.9163 (mt) cc_final: 0.8947 (mt) REVERT: C 717 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7436 (mp) REVERT: D 555 ARG cc_start: 0.8693 (ttp-110) cc_final: 0.8329 (ptp-170) REVERT: D 657 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8008 (ttmt) REVERT: D 716 TYR cc_start: 0.8047 (m-10) cc_final: 0.7716 (m-80) REVERT: D 719 ASP cc_start: 0.6967 (t0) cc_final: 0.6659 (t70) REVERT: E 366 THR cc_start: 0.9527 (m) cc_final: 0.9078 (p) REVERT: F 339 MET cc_start: 0.8096 (tpp) cc_final: 0.7774 (tpp) REVERT: F 484 LEU cc_start: 0.9637 (mt) cc_final: 0.9367 (mt) REVERT: F 645 ASN cc_start: 0.8065 (m-40) cc_final: 0.7676 (t0) REVERT: F 653 GLN cc_start: 0.8787 (tt0) cc_final: 0.8530 (tt0) outliers start: 82 outliers final: 63 residues processed: 372 average time/residue: 0.1146 time to fit residues: 70.1393 Evaluate side-chains 380 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 315 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 675 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 601 MET Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 452 ILE Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain E residue 701 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 593 VAL Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 696 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 224 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 221 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN F 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096070 restraints weight = 36345.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098107 restraints weight = 23969.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098852 restraints weight = 18226.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099878 restraints weight = 14683.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099943 restraints weight = 13688.337| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19190 Z= 0.123 Angle : 0.697 10.615 26169 Z= 0.333 Chirality : 0.046 0.197 3128 Planarity : 0.004 0.056 3227 Dihedral : 14.091 174.877 2908 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.09 % Allowed : 19.29 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2350 helix: 0.68 (0.17), residues: 972 sheet: -0.73 (0.25), residues: 370 loop : -1.49 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 555 TYR 0.028 0.002 TYR D 432 PHE 0.036 0.002 PHE E 553 TRP 0.023 0.002 TRP D 530 HIS 0.012 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (19190) covalent geometry : angle 0.69740 / 0.33 (26169) hydrogen bonds : bond 0.03486 / 2.30 ( 801) hydrogen bonds : angle 4.90507 / 3.38 ( 2269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 350 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8636 (tpp) cc_final: 0.8269 (tpp) REVERT: A 610 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 624 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8878 (mp) REVERT: A 680 TYR cc_start: 0.8718 (t80) cc_final: 0.8456 (t80) REVERT: A 701 VAL cc_start: 0.9263 (t) cc_final: 0.8953 (p) REVERT: B 383 ASN cc_start: 0.8094 (t0) cc_final: 0.7876 (t0) REVERT: B 400 VAL cc_start: 0.8972 (t) cc_final: 0.8731 (m) REVERT: B 419 GLN cc_start: 0.7643 (tt0) cc_final: 0.7077 (mt0) REVERT: B 481 LEU cc_start: 0.9254 (mp) cc_final: 0.8977 (tt) REVERT: B 540 ARG cc_start: 0.7813 (mtm180) cc_final: 0.6879 (mmt90) REVERT: C 455 ASP cc_start: 0.8319 (t0) cc_final: 0.7768 (t0) REVERT: C 521 MET cc_start: 0.7703 (mmt) cc_final: 0.6751 (mmt) REVERT: C 672 LEU cc_start: 0.9111 (mt) cc_final: 0.8889 (mt) REVERT: C 717 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7405 (mp) REVERT: D 507 TYR cc_start: 0.8235 (m-80) cc_final: 0.7814 (m-80) REVERT: D 547 VAL cc_start: 0.8433 (t) cc_final: 0.8145 (p) REVERT: D 555 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.8178 (ptp-170) REVERT: D 657 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8029 (ttmt) REVERT: D 659 ASP cc_start: 0.7674 (m-30) cc_final: 0.7448 (m-30) REVERT: D 662 THR cc_start: 0.8702 (m) cc_final: 0.8238 (p) REVERT: D 716 TYR cc_start: 0.7816 (m-10) cc_final: 0.7523 (m-10) REVERT: D 719 ASP cc_start: 0.6778 (t0) cc_final: 0.6488 (t70) REVERT: E 366 THR cc_start: 0.9411 (m) cc_final: 0.8982 (p) REVERT: E 628 LEU cc_start: 0.9491 (mt) cc_final: 0.9213 (mt) REVERT: F 484 LEU cc_start: 0.9619 (mt) cc_final: 0.9298 (mp) outliers start: 62 outliers final: 44 residues processed: 386 average time/residue: 0.1207 time to fit residues: 76.0223 Evaluate side-chains 374 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 675 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 452 ILE Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 677 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 86 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN D 671 GLN F 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095986 restraints weight = 36248.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098198 restraints weight = 24576.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099093 restraints weight = 17995.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100503 restraints weight = 14284.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100451 restraints weight = 12944.073| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19190 Z= 0.128 Angle : 0.700 11.555 26169 Z= 0.333 Chirality : 0.046 0.191 3128 Planarity : 0.004 0.055 3227 Dihedral : 13.931 166.735 2908 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.54 % Allowed : 19.79 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2350 helix: 0.77 (0.17), residues: 967 sheet: -0.57 (0.25), residues: 380 loop : -1.43 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 555 TYR 0.026 0.002 TYR D 432 PHE 0.037 0.002 PHE E 553 TRP 0.025 0.002 TRP D 530 HIS 0.011 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19190) covalent geometry : angle 0.70049 / 0.33 (26169) hydrogen bonds : bond 0.03484 / 2.32 ( 801) hydrogen bonds : angle 4.86092 / 3.35 ( 2269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 0.755 Fit side-chains REVERT: A 535 MET cc_start: 0.8619 (tpp) cc_final: 0.8311 (tpp) REVERT: A 610 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 624 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8837 (mp) REVERT: A 680 TYR cc_start: 0.8691 (t80) cc_final: 0.8466 (t80) REVERT: A 701 VAL cc_start: 0.9285 (t) cc_final: 0.8992 (p) REVERT: B 383 ASN cc_start: 0.8110 (t0) cc_final: 0.7894 (t0) REVERT: B 419 GLN cc_start: 0.7627 (tt0) cc_final: 0.7077 (mt0) REVERT: B 481 LEU cc_start: 0.9246 (mp) cc_final: 0.8964 (tt) REVERT: B 540 ARG cc_start: 0.7813 (mtm180) cc_final: 0.6900 (mmt90) REVERT: C 455 ASP cc_start: 0.8247 (t0) cc_final: 0.7720 (t0) REVERT: C 521 MET cc_start: 0.7628 (mmt) cc_final: 0.6721 (mmt) REVERT: C 672 LEU cc_start: 0.9078 (mt) cc_final: 0.8847 (mt) REVERT: C 717 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7390 (mp) REVERT: D 507 TYR cc_start: 0.8165 (m-80) cc_final: 0.7721 (m-80) REVERT: D 542 MET cc_start: 0.8145 (ptp) cc_final: 0.7888 (ptm) REVERT: D 547 VAL cc_start: 0.8408 (t) cc_final: 0.7601 (p) REVERT: D 555 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8180 (ptp-170) REVERT: D 657 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8005 (ttmt) REVERT: D 659 ASP cc_start: 0.7669 (m-30) cc_final: 0.7409 (m-30) REVERT: D 662 THR cc_start: 0.8679 (m) cc_final: 0.8222 (p) REVERT: D 716 TYR cc_start: 0.7785 (m-10) cc_final: 0.7421 (m-10) REVERT: D 719 ASP cc_start: 0.6768 (t0) cc_final: 0.6457 (t70) REVERT: E 366 THR cc_start: 0.9407 (m) cc_final: 0.8976 (p) REVERT: E 617 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7753 (tm-30) REVERT: E 628 LEU cc_start: 0.9509 (mt) cc_final: 0.9225 (mt) REVERT: E 631 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8447 (mm-40) REVERT: F 484 LEU cc_start: 0.9606 (mt) cc_final: 0.9293 (mt) outliers start: 51 outliers final: 41 residues processed: 366 average time/residue: 0.1167 time to fit residues: 70.6217 Evaluate side-chains 367 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 675 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 696 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 171 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 77 optimal weight: 0.1980 chunk 57 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN D 671 GLN F 702 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095200 restraints weight = 36910.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.096834 restraints weight = 23979.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.097830 restraints weight = 17882.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099456 restraints weight = 14647.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099449 restraints weight = 12970.340| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19190 Z= 0.167 Angle : 0.720 12.166 26169 Z= 0.344 Chirality : 0.047 0.192 3128 Planarity : 0.004 0.054 3227 Dihedral : 13.870 163.484 2908 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.89 % Allowed : 19.74 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2350 helix: 0.79 (0.17), residues: 960 sheet: -0.44 (0.25), residues: 388 loop : -1.38 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 555 TYR 0.025 0.002 TYR B 539 PHE 0.046 0.002 PHE E 553 TRP 0.025 0.002 TRP D 530 HIS 0.011 0.001 HIS F 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (19190) covalent geometry : angle 0.72033 / 0.34 (26169) hydrogen bonds : bond 0.03541 / 2.35 ( 801) hydrogen bonds : angle 4.87340 / 3.36 ( 2269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.29 seconds wall clock time: 49 minutes 48.01 seconds (2988.01 seconds total)