Starting phenix.real_space_refine on Thu Mar 5 03:14:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t8o_10402/03_2026/6t8o_10402.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t8o_10402/03_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_10402/03_2026/6t8o_10402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t8o_10402/03_2026/6t8o_10402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t8o_10402/03_2026/6t8o_10402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t8o_10402/03_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-dev-5986/lib/python3.9/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: 4.54, per 1000 atoms: 0.24 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: 1.44 Conformation dependent library (CDL) restraints added in 792.9 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: 2.34 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: 3.02 Time building geometry restraints manager: 1.94 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=" 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 bond pdb=" C ALA A 713 " pdb=" N PRO A 714 " ideal model delta sigma weight residual 1.333 1.351 -0.017 1.01e-02 9.80e+03 3.00e+00 bond pdb=" C ALA D 713 " pdb=" N PRO D 714 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.67e+00 bond pdb=" CG LEU D 384 " pdb=" CD2 LEU D 384 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 ... (remaining 19185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 25588 2.56 - 5.13: 512 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: 2225 0.052 - 0.104: 683 0.104 - 0.156: 189 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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= 0.238 Angle : 0.913 12.819 26169 Z= 0.475 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 covalent geometry : bond 0.00562 (19190) covalent geometry : angle 0.91264 (26169) hydrogen bonds : bond 0.16342 ( 801) hydrogen bonds : angle 7.06526 ( 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 : 0.690 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: 0.1648 time to fit residues: 158.4986 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 : 0.848 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 435 HIS A 461 HIS A 512 HIS A 666 GLN B 631 GLN B 645 ASN C 645 ASN C 666 GLN C 692 HIS C 702 HIS D 383 ASN D 435 HIS D 666 GLN E 435 HIS E 445 HIS F 477 ASN F 512 HIS F 549 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095162 restraints weight = 36720.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097460 restraints weight = 23965.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098660 restraints weight = 17567.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099993 restraints weight = 13481.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099982 restraints weight = 11858.915| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19190 Z= 0.160 Angle : 0.699 9.149 26169 Z= 0.344 Chirality : 0.046 0.166 3128 Planarity : 0.005 0.048 3227 Dihedral : 14.872 176.901 2908 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.74 % Allowed : 14.06 % Favored : 83.20 % 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: -2.38 (0.16), residues: 2350 helix: -0.79 (0.15), residues: 964 sheet: -1.49 (0.24), residues: 373 loop : -2.34 (0.17), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 614 TYR 0.019 0.002 TYR C 507 PHE 0.014 0.002 PHE F 597 TRP 0.020 0.002 TRP E 530 HIS 0.008 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00364 (19190) covalent geometry : angle 0.69856 (26169) hydrogen bonds : bond 0.04158 ( 801) hydrogen bonds : angle 5.27970 ( 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 486 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 431 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7268 (m-70) cc_final: 0.6841 (m170) REVERT: A 369 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6735 (mt-10) REVERT: A 535 MET cc_start: 0.8703 (ttp) cc_final: 0.8443 (ttt) REVERT: A 539 TYR cc_start: 0.8612 (m-80) cc_final: 0.8332 (m-10) REVERT: A 638 ILE cc_start: 0.7791 (mt) cc_final: 0.7507 (pt) REVERT: B 540 ARG cc_start: 0.7962 (mtm180) cc_final: 0.6886 (mtp85) REVERT: C 454 THR cc_start: 0.9372 (p) cc_final: 0.9158 (t) REVERT: C 521 MET cc_start: 0.7791 (mmt) cc_final: 0.6841 (mmt) REVERT: C 648 THR cc_start: 0.9408 (m) cc_final: 0.9077 (p) REVERT: D 455 ASP cc_start: 0.8413 (t0) cc_final: 0.8043 (m-30) REVERT: D 479 MET cc_start: 0.8378 (mtm) cc_final: 0.8173 (mtt) REVERT: D 555 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8275 (ptp-170) REVERT: D 599 ASP cc_start: 0.7538 (m-30) cc_final: 0.6963 (m-30) REVERT: D 601 MET cc_start: 0.8813 (mtm) cc_final: 0.8502 (mtm) REVERT: D 609 GLU cc_start: 0.8202 (tt0) cc_final: 0.7980 (tt0) REVERT: D 662 THR cc_start: 0.8316 (m) cc_final: 0.7916 (p) REVERT: D 675 HIS cc_start: 0.6900 (m-70) cc_final: 0.6632 (m-70) REVERT: D 719 ASP cc_start: 0.7107 (t0) cc_final: 0.6587 (t70) REVERT: E 366 THR cc_start: 0.9473 (m) cc_final: 0.9097 (p) REVERT: E 701 VAL cc_start: 0.9562 (t) cc_final: 0.9299 (p) REVERT: F 498 ASP cc_start: 0.8763 (t0) cc_final: 0.8477 (t0) REVERT: F 658 ILE cc_start: 0.8251 (mp) cc_final: 0.7932 (mm) outliers start: 55 outliers final: 25 residues processed: 463 average time/residue: 0.1314 time to fit residues: 94.6775 Evaluate side-chains 372 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 347 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 THR 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 392 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 617 GLN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 396 SER 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 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 407 THR 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: 7.9990 chunk 223 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 625 HIS A 666 GLN C 653 GLN D 671 GLN E 383 ASN E 445 HIS E 631 GLN ** 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 = 0.3508 r_free = 0.3508 target = 0.119068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095099 restraints weight = 36532.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097110 restraints weight = 25319.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098102 restraints weight = 19042.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099668 restraints weight = 14897.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099644 restraints weight = 13032.251| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19190 Z= 0.156 Angle : 0.664 8.309 26169 Z= 0.324 Chirality : 0.045 0.182 3128 Planarity : 0.005 0.064 3227 Dihedral : 14.502 179.776 2908 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.64 % Allowed : 15.60 % Favored : 80.76 % 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: -1.62 (0.16), residues: 2350 helix: -0.03 (0.16), residues: 972 sheet: -1.18 (0.24), residues: 387 loop : -2.05 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 540 TYR 0.020 0.002 TYR E 432 PHE 0.019 0.002 PHE B 597 TRP 0.016 0.002 TRP E 530 HIS 0.010 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00359 (19190) covalent geometry : angle 0.66412 (26169) hydrogen bonds : bond 0.03690 ( 801) hydrogen bonds : angle 5.00026 ( 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 452 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 379 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7299 (m-70) cc_final: 0.6845 (m170) REVERT: A 369 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 587 LEU cc_start: 0.8675 (mt) cc_final: 0.8140 (mt) REVERT: A 607 LYS cc_start: 0.7764 (pptt) cc_final: 0.7489 (ptmt) REVERT: A 701 VAL cc_start: 0.9178 (t) cc_final: 0.8812 (p) REVERT: B 419 GLN cc_start: 0.7730 (tt0) cc_final: 0.7074 (mt0) REVERT: B 477 ASN cc_start: 0.9018 (m-40) cc_final: 0.8776 (t0) REVERT: B 540 ARG cc_start: 0.7889 (mtm180) cc_final: 0.6851 (mtp85) REVERT: C 455 ASP cc_start: 0.8313 (t0) cc_final: 0.7813 (t0) REVERT: C 459 MET cc_start: 0.8727 (mmm) cc_final: 0.8405 (mmm) REVERT: C 484 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9118 (mm) REVERT: C 517 VAL cc_start: 0.9135 (t) cc_final: 0.8917 (m) REVERT: C 609 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: C 648 THR cc_start: 0.9358 (m) cc_final: 0.9079 (p) REVERT: C 650 ILE cc_start: 0.9431 (mm) cc_final: 0.9159 (mt) REVERT: C 706 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7017 (pt0) REVERT: D 535 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8651 (ttt) REVERT: D 555 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8284 (ptp-170) REVERT: D 601 MET cc_start: 0.8714 (mtm) cc_final: 0.8467 (mtm) REVERT: D 609 GLU cc_start: 0.8183 (tt0) cc_final: 0.7954 (tt0) REVERT: D 617 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8295 (tm-30) REVERT: D 657 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8305 (ttmt) REVERT: D 662 THR cc_start: 0.8337 (m) cc_final: 0.7972 (p) REVERT: D 719 ASP cc_start: 0.7133 (t0) cc_final: 0.6793 (t70) REVERT: E 366 THR cc_start: 0.9465 (m) cc_final: 0.9100 (p) REVERT: F 420 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6754 (mtp) REVERT: F 456 LEU cc_start: 0.9050 (tp) cc_final: 0.8748 (tp) REVERT: F 484 LEU cc_start: 0.9599 (mt) cc_final: 0.9291 (mt) REVERT: F 498 ASP cc_start: 0.8571 (t0) cc_final: 0.8311 (t0) REVERT: F 535 MET cc_start: 0.8977 (ttp) cc_final: 0.8718 (ttp) REVERT: F 602 MET cc_start: 0.7460 (tmm) cc_final: 0.7221 (mmp) REVERT: F 658 ILE cc_start: 0.8250 (mp) cc_final: 0.8009 (mm) outliers start: 73 outliers final: 42 residues processed: 427 average time/residue: 0.1275 time to fit residues: 86.4886 Evaluate side-chains 367 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 321 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 382 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 600 MET Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 617 GLN Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 321 LEU 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 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 407 THR 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 483 ILE Chi-restraints excluded: chain F residue 526 ASN 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: 5.9990 chunk 230 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN D 671 GLN E 371 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 HIS F 702 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096349 restraints weight = 36519.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099065 restraints weight = 24012.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099647 restraints weight = 18138.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100633 restraints weight = 14235.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100860 restraints weight = 12860.832| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19190 Z= 0.121 Angle : 0.643 7.493 26169 Z= 0.310 Chirality : 0.045 0.151 3128 Planarity : 0.004 0.048 3227 Dihedral : 14.101 178.269 2908 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.34 % Allowed : 17.10 % Favored : 79.56 % 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: -1.15 (0.17), residues: 2350 helix: 0.34 (0.17), residues: 963 sheet: -0.94 (0.24), residues: 386 loop : -1.76 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 538 TYR 0.020 0.002 TYR E 432 PHE 0.023 0.001 PHE E 553 TRP 0.010 0.001 TRP E 530 HIS 0.010 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00276 (19190) covalent geometry : angle 0.64334 (26169) hydrogen bonds : bond 0.03345 ( 801) hydrogen bonds : angle 4.80355 ( 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 443 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 376 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7325 (m-70) cc_final: 0.6848 (m170) REVERT: A 369 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 445 HIS cc_start: 0.8426 (m-70) cc_final: 0.8129 (m-70) REVERT: A 461 HIS cc_start: 0.8299 (m-70) cc_final: 0.7919 (m-70) REVERT: A 462 LEU cc_start: 0.8951 (tp) cc_final: 0.8702 (tt) REVERT: A 607 LYS cc_start: 0.7689 (pptt) cc_final: 0.7480 (ptmt) REVERT: A 701 VAL cc_start: 0.9245 (t) cc_final: 0.8908 (p) REVERT: B 419 GLN cc_start: 0.7724 (tt0) cc_final: 0.7051 (mt0) REVERT: B 479 MET cc_start: 0.8655 (mtp) cc_final: 0.8253 (mmt) REVERT: B 481 LEU cc_start: 0.9198 (mp) cc_final: 0.8820 (tt) REVERT: B 540 ARG cc_start: 0.7814 (mtm180) cc_final: 0.6818 (mtp85) REVERT: C 455 ASP cc_start: 0.8222 (t0) cc_final: 0.7728 (t0) REVERT: C 484 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9134 (mm) REVERT: C 517 VAL cc_start: 0.9167 (t) cc_final: 0.8966 (m) REVERT: C 650 ILE cc_start: 0.9431 (mm) cc_final: 0.9133 (mt) REVERT: C 672 LEU cc_start: 0.9219 (mt) cc_final: 0.8855 (mt) REVERT: C 706 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7181 (pt0) REVERT: D 459 MET cc_start: 0.8268 (mmm) cc_final: 0.7967 (mmm) REVERT: D 496 MET cc_start: 0.8548 (mmp) cc_final: 0.8201 (mmt) REVERT: D 542 MET cc_start: 0.8261 (ptp) cc_final: 0.7903 (ptm) REVERT: D 547 VAL cc_start: 0.8468 (t) cc_final: 0.7637 (p) REVERT: D 555 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8302 (ptp-170) REVERT: D 601 MET cc_start: 0.8709 (mtm) cc_final: 0.8485 (mtm) REVERT: D 609 GLU cc_start: 0.8238 (tt0) cc_final: 0.7983 (tt0) REVERT: D 617 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8406 (tm-30) REVERT: D 657 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8356 (ttmt) REVERT: D 659 ASP cc_start: 0.7764 (m-30) cc_final: 0.7454 (m-30) REVERT: D 662 THR cc_start: 0.8329 (m) cc_final: 0.7993 (p) REVERT: D 716 TYR cc_start: 0.7892 (m-10) cc_final: 0.7348 (m-10) REVERT: D 719 ASP cc_start: 0.6964 (t0) cc_final: 0.6668 (t70) REVERT: E 366 THR cc_start: 0.9411 (m) cc_final: 0.9061 (p) REVERT: E 628 LEU cc_start: 0.9513 (mt) cc_final: 0.9243 (mt) REVERT: F 456 LEU cc_start: 0.8994 (tp) cc_final: 0.8787 (tp) REVERT: F 484 LEU cc_start: 0.9603 (mt) cc_final: 0.9300 (mt) REVERT: F 535 MET cc_start: 0.9002 (ttp) cc_final: 0.8709 (ttp) REVERT: F 602 MET cc_start: 0.7429 (tmm) cc_final: 0.7107 (mmp) outliers start: 67 outliers final: 45 residues processed: 417 average time/residue: 0.1178 time to fit residues: 79.6618 Evaluate side-chains 385 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 339 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 495 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 402 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 484 LEU Chi-restraints excluded: chain B residue 530 TRP 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 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 617 GLN Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 488 THR 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 409 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 526 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 77 optimal weight: 0.0970 chunk 164 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN B 625 HIS C 435 HIS D 671 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094923 restraints weight = 36479.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097265 restraints weight = 23951.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098223 restraints weight = 17227.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098705 restraints weight = 14086.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098821 restraints weight = 13852.352| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19190 Z= 0.162 Angle : 0.653 7.362 26169 Z= 0.316 Chirality : 0.046 0.187 3128 Planarity : 0.004 0.044 3227 Dihedral : 13.855 174.539 2908 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.39 % Allowed : 16.40 % Favored : 79.21 % 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: -0.89 (0.17), residues: 2350 helix: 0.49 (0.17), residues: 974 sheet: -0.70 (0.24), residues: 385 loop : -1.62 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 555 TYR 0.020 0.002 TYR E 432 PHE 0.017 0.002 PHE D 553 TRP 0.013 0.001 TRP D 530 HIS 0.010 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00377 (19190) covalent geometry : angle 0.65312 (26169) hydrogen bonds : bond 0.03400 ( 801) hydrogen bonds : angle 4.78387 ( 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 436 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 348 time to evaluate : 0.681 Fit side-chains REVERT: A 360 HIS cc_start: 0.7327 (m-70) cc_final: 0.6856 (m170) REVERT: A 369 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 445 HIS cc_start: 0.8301 (m-70) cc_final: 0.8017 (m-70) REVERT: A 539 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: A 607 LYS cc_start: 0.7726 (pptt) cc_final: 0.7477 (ptmt) REVERT: A 701 VAL cc_start: 0.9306 (t) cc_final: 0.9009 (p) REVERT: B 419 GLN cc_start: 0.7665 (tt0) cc_final: 0.7007 (mt0) REVERT: B 477 ASN cc_start: 0.8909 (m-40) cc_final: 0.8701 (t0) REVERT: B 479 MET cc_start: 0.8601 (mtp) cc_final: 0.8188 (mmt) REVERT: B 481 LEU cc_start: 0.9252 (mp) cc_final: 0.8866 (tt) REVERT: B 540 ARG cc_start: 0.7860 (mtm180) cc_final: 0.6823 (mtp85) REVERT: C 455 ASP cc_start: 0.8293 (t0) cc_final: 0.7839 (t0) REVERT: C 484 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9179 (mm) REVERT: C 521 MET cc_start: 0.7767 (mmt) cc_final: 0.6736 (mmt) REVERT: C 650 ILE cc_start: 0.9477 (mm) cc_final: 0.9249 (mt) REVERT: C 706 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7072 (pt0) REVERT: C 717 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7282 (mp) REVERT: D 434 GLU cc_start: 0.7188 (tp30) cc_final: 0.6927 (tp30) REVERT: D 547 VAL cc_start: 0.8453 (t) cc_final: 0.8130 (p) REVERT: D 555 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8310 (ptp-170) REVERT: D 609 GLU cc_start: 0.8190 (tt0) cc_final: 0.7911 (tt0) REVERT: D 617 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 657 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8208 (ttmt) REVERT: D 716 TYR cc_start: 0.7903 (m-10) cc_final: 0.7616 (m-80) REVERT: D 719 ASP cc_start: 0.6927 (t0) cc_final: 0.6602 (t70) REVERT: E 366 THR cc_start: 0.9365 (m) cc_final: 0.8974 (p) REVERT: E 617 GLN cc_start: 0.7767 (tp40) cc_final: 0.7323 (tp40) REVERT: E 631 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8467 (mm-40) REVERT: F 339 MET cc_start: 0.8080 (tpp) cc_final: 0.7751 (tpp) REVERT: F 535 MET cc_start: 0.9020 (ttp) cc_final: 0.8723 (ttp) REVERT: F 602 MET cc_start: 0.7411 (tmm) cc_final: 0.6934 (mmp) REVERT: F 645 ASN cc_start: 0.8101 (m-40) cc_final: 0.7662 (t0) outliers start: 88 outliers final: 58 residues processed: 404 average time/residue: 0.1180 time to fit residues: 77.2128 Evaluate side-chains 387 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 326 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 408 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 495 ILE Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP 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 484 LEU Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 591 VAL 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 C residue 720 ILE Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 608 VAL 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 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 526 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 75 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN D 383 ASN D 477 ASN E 631 GLN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.093727 restraints weight = 36434.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095767 restraints weight = 24502.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096627 restraints weight = 17839.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096990 restraints weight = 14762.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097323 restraints weight = 14287.558| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19190 Z= 0.186 Angle : 0.684 8.282 26169 Z= 0.329 Chirality : 0.047 0.379 3128 Planarity : 0.004 0.047 3227 Dihedral : 13.730 169.563 2908 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.54 % Allowed : 17.60 % Favored : 77.87 % 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: -0.68 (0.17), residues: 2350 helix: 0.72 (0.17), residues: 953 sheet: -0.62 (0.24), residues: 389 loop : -1.51 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 690 TYR 0.020 0.002 TYR E 432 PHE 0.027 0.002 PHE E 553 TRP 0.014 0.002 TRP D 530 HIS 0.010 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00433 (19190) covalent geometry : angle 0.68360 (26169) hydrogen bonds : bond 0.03522 ( 801) hydrogen bonds : angle 4.81303 ( 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 431 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 340 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7308 (m-70) cc_final: 0.6823 (m170) REVERT: A 369 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 445 HIS cc_start: 0.8374 (m-70) cc_final: 0.8112 (m-70) REVERT: A 539 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: A 596 GLU cc_start: 0.7939 (tp30) cc_final: 0.7731 (tm-30) REVERT: A 610 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 701 VAL cc_start: 0.9371 (t) cc_final: 0.9079 (p) REVERT: B 419 GLN cc_start: 0.7646 (tt0) cc_final: 0.6990 (mt0) REVERT: B 479 MET cc_start: 0.8647 (mtp) cc_final: 0.8365 (tpp) REVERT: B 481 LEU cc_start: 0.9290 (mp) cc_final: 0.8929 (tt) REVERT: B 540 ARG cc_start: 0.7828 (mtm180) cc_final: 0.6918 (mmt-90) REVERT: C 455 ASP cc_start: 0.8364 (t0) cc_final: 0.7903 (t0) REVERT: C 484 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9172 (mm) REVERT: C 521 MET cc_start: 0.7773 (mmt) cc_final: 0.6785 (mmt) REVERT: C 650 ILE cc_start: 0.9470 (mm) cc_final: 0.9254 (mt) REVERT: D 434 GLU cc_start: 0.7179 (tp30) cc_final: 0.6903 (tp30) REVERT: D 547 VAL cc_start: 0.8474 (t) cc_final: 0.8168 (p) REVERT: D 555 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8343 (ptp-170) REVERT: D 609 GLU cc_start: 0.8187 (tt0) cc_final: 0.7931 (tt0) REVERT: D 657 LYS cc_start: 0.8683 (mtmt) cc_final: 0.7941 (ttmt) REVERT: D 662 THR cc_start: 0.8715 (m) cc_final: 0.8270 (p) REVERT: D 716 TYR cc_start: 0.7940 (m-10) cc_final: 0.7621 (m-80) REVERT: D 719 ASP cc_start: 0.6978 (t0) cc_final: 0.6660 (t70) REVERT: E 366 THR cc_start: 0.9395 (m) cc_final: 0.8993 (p) REVERT: E 600 MET cc_start: 0.7979 (ttm) cc_final: 0.7741 (mtt) REVERT: F 539 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8484 (m-10) REVERT: F 602 MET cc_start: 0.7405 (tmm) cc_final: 0.7057 (mmp) outliers start: 91 outliers final: 69 residues processed: 401 average time/residue: 0.1168 time to fit residues: 76.6871 Evaluate side-chains 395 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 323 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 408 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 603 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 A residue 696 VAL Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP 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 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 MET 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 720 ILE Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 717 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 488 THR Chi-restraints excluded: chain E residue 586 THR Chi-restraints excluded: chain E residue 608 VAL 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 402 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 539 TYR 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 637 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 98 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN C 435 HIS E 383 ASN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095449 restraints weight = 36523.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097930 restraints weight = 23774.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098744 restraints weight = 17901.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099942 restraints weight = 13894.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100040 restraints weight = 12533.964| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19190 Z= 0.132 Angle : 0.651 7.754 26169 Z= 0.313 Chirality : 0.046 0.319 3128 Planarity : 0.004 0.052 3227 Dihedral : 13.567 163.366 2908 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.69 % Allowed : 18.79 % Favored : 77.52 % 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: -0.54 (0.17), residues: 2350 helix: 0.83 (0.17), residues: 966 sheet: -0.57 (0.25), residues: 379 loop : -1.42 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 555 TYR 0.019 0.001 TYR E 432 PHE 0.023 0.001 PHE B 553 TRP 0.018 0.001 TRP D 530 HIS 0.011 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00306 (19190) covalent geometry : angle 0.65144 (26169) hydrogen bonds : bond 0.03319 ( 801) hydrogen bonds : angle 4.71946 ( 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 424 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 350 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7386 (m-70) cc_final: 0.6688 (m170) REVERT: A 369 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6935 (mt-10) REVERT: A 445 HIS cc_start: 0.8400 (m-70) cc_final: 0.8115 (m-70) REVERT: A 539 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: A 701 VAL cc_start: 0.9363 (t) cc_final: 0.9074 (p) REVERT: B 419 GLN cc_start: 0.7604 (tt0) cc_final: 0.6941 (mt0) REVERT: B 479 MET cc_start: 0.8721 (mtp) cc_final: 0.8417 (tpp) REVERT: B 481 LEU cc_start: 0.9256 (mp) cc_final: 0.8889 (tt) REVERT: B 540 ARG cc_start: 0.7818 (mtm180) cc_final: 0.6762 (mtp85) REVERT: B 601 MET cc_start: 0.6754 (ttp) cc_final: 0.6493 (ttp) REVERT: C 455 ASP cc_start: 0.8306 (t0) cc_final: 0.7846 (t0) REVERT: C 484 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9156 (mm) REVERT: C 521 MET cc_start: 0.7832 (mmt) cc_final: 0.6684 (mmt) REVERT: C 650 ILE cc_start: 0.9474 (mm) cc_final: 0.9225 (mt) REVERT: C 672 LEU cc_start: 0.9184 (mt) cc_final: 0.8969 (mt) REVERT: D 434 GLU cc_start: 0.7023 (tp30) cc_final: 0.6759 (tp30) REVERT: D 547 VAL cc_start: 0.8453 (t) cc_final: 0.8140 (p) REVERT: D 555 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8226 (ptp-170) REVERT: D 609 GLU cc_start: 0.8165 (tt0) cc_final: 0.7914 (tt0) REVERT: D 657 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8202 (ttmt) REVERT: D 659 ASP cc_start: 0.7694 (m-30) cc_final: 0.7434 (m-30) REVERT: D 662 THR cc_start: 0.8665 (m) cc_final: 0.8235 (p) REVERT: D 716 TYR cc_start: 0.7737 (m-10) cc_final: 0.7334 (m-10) REVERT: D 719 ASP cc_start: 0.6927 (t0) cc_final: 0.6617 (t70) REVERT: E 366 THR cc_start: 0.9370 (m) cc_final: 0.8984 (p) REVERT: E 600 MET cc_start: 0.8084 (ttm) cc_final: 0.7779 (mtt) REVERT: F 498 ASP cc_start: 0.8515 (t0) cc_final: 0.8195 (t0) REVERT: F 539 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8511 (m-10) outliers start: 74 outliers final: 58 residues processed: 399 average time/residue: 0.1230 time to fit residues: 78.7575 Evaluate side-chains 389 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 328 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 539 TYR 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 A residue 696 VAL Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 678 MET 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 454 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 SER 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 689 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 436 LYS Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 720 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 488 THR 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 356 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 526 ASN Chi-restraints excluded: chain F residue 539 TYR Chi-restraints excluded: chain F residue 612 ILE Chi-restraints excluded: chain F residue 637 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 15 optimal weight: 0.0270 chunk 211 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN F 419 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 = 0.3551 r_free = 0.3551 target = 0.122139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097521 restraints weight = 36459.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099721 restraints weight = 24620.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100739 restraints weight = 18835.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101594 restraints weight = 14456.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101836 restraints weight = 13055.836| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19190 Z= 0.112 Angle : 0.649 8.942 26169 Z= 0.308 Chirality : 0.045 0.271 3128 Planarity : 0.004 0.049 3227 Dihedral : 13.365 170.995 2908 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.39 % Allowed : 18.89 % Favored : 77.72 % 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: -0.39 (0.18), residues: 2350 helix: 0.98 (0.18), residues: 961 sheet: -0.57 (0.25), residues: 379 loop : -1.34 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 555 TYR 0.022 0.001 TYR B 539 PHE 0.015 0.001 PHE F 597 TRP 0.023 0.001 TRP D 530 HIS 0.012 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00257 (19190) covalent geometry : angle 0.64885 (26169) hydrogen bonds : bond 0.03170 ( 801) hydrogen bonds : angle 4.61830 ( 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 435 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 367 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7298 (m-70) cc_final: 0.6575 (m170) REVERT: A 369 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 445 HIS cc_start: 0.8388 (m-70) cc_final: 0.8113 (m-70) REVERT: A 462 LEU cc_start: 0.9061 (mt) cc_final: 0.8694 (mp) REVERT: A 535 MET cc_start: 0.8360 (ttt) cc_final: 0.8077 (ttt) REVERT: A 607 LYS cc_start: 0.7753 (pptt) cc_final: 0.7490 (ptmt) REVERT: A 701 VAL cc_start: 0.9346 (t) cc_final: 0.9061 (p) REVERT: B 419 GLN cc_start: 0.7629 (tt0) cc_final: 0.6860 (mt0) REVERT: B 502 LEU cc_start: 0.7101 (pt) cc_final: 0.6300 (pp) REVERT: B 540 ARG cc_start: 0.7773 (mtm180) cc_final: 0.6881 (mmt-90) REVERT: B 545 MET cc_start: 0.6809 (ptp) cc_final: 0.6602 (ptp) REVERT: B 680 TYR cc_start: 0.8288 (t80) cc_final: 0.7873 (t80) REVERT: C 455 ASP cc_start: 0.8213 (t0) cc_final: 0.7791 (t0) REVERT: C 484 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9128 (mm) REVERT: C 650 ILE cc_start: 0.9430 (mm) cc_final: 0.9149 (mt) REVERT: C 672 LEU cc_start: 0.9082 (mt) cc_final: 0.8833 (mt) REVERT: C 706 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7200 (pt0) REVERT: D 420 MET cc_start: 0.6937 (ttp) cc_final: 0.6713 (ttp) REVERT: D 434 GLU cc_start: 0.6955 (tp30) cc_final: 0.6699 (tp30) REVERT: D 547 VAL cc_start: 0.8406 (t) cc_final: 0.8070 (p) REVERT: D 555 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8231 (ptp-170) REVERT: D 609 GLU cc_start: 0.8159 (tt0) cc_final: 0.7940 (tt0) REVERT: D 612 ILE cc_start: 0.9061 (mm) cc_final: 0.8840 (mt) REVERT: D 657 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8255 (ttmt) REVERT: D 659 ASP cc_start: 0.7599 (m-30) cc_final: 0.7351 (m-30) REVERT: D 661 ARG cc_start: 0.7680 (mtt90) cc_final: 0.7419 (ptp-110) REVERT: D 662 THR cc_start: 0.8632 (m) cc_final: 0.8239 (p) REVERT: D 716 TYR cc_start: 0.7664 (m-10) cc_final: 0.7308 (m-10) REVERT: D 719 ASP cc_start: 0.6825 (t0) cc_final: 0.6525 (t70) REVERT: E 631 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8305 (mm-40) REVERT: F 539 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8507 (m-10) REVERT: F 675 HIS cc_start: 0.6563 (m-70) cc_final: 0.5695 (m-70) outliers start: 68 outliers final: 54 residues processed: 413 average time/residue: 0.1254 time to fit residues: 82.4057 Evaluate side-chains 388 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 332 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 441 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 539 TYR 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 A residue 696 VAL Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 678 MET 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 484 LEU Chi-restraints excluded: chain C residue 487 SER 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 720 ILE Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 356 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 483 ILE Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 539 TYR Chi-restraints excluded: chain F residue 593 VAL Chi-restraints excluded: chain F residue 637 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 224 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 118 optimal weight: 0.0050 chunk 221 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 207 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 666 GLN E 371 GLN F 702 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098611 restraints weight = 36226.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100797 restraints weight = 23483.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102324 restraints weight = 17340.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103400 restraints weight = 14018.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104073 restraints weight = 12065.683| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19190 Z= 0.112 Angle : 0.662 11.102 26169 Z= 0.313 Chirality : 0.045 0.182 3128 Planarity : 0.004 0.044 3227 Dihedral : 13.167 174.271 2908 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.09 % Allowed : 19.94 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2350 helix: 1.04 (0.18), residues: 955 sheet: -0.26 (0.25), residues: 389 loop : -1.29 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 555 TYR 0.019 0.001 TYR C 432 PHE 0.027 0.001 PHE D 553 TRP 0.018 0.001 TRP D 530 HIS 0.012 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00254 (19190) covalent geometry : angle 0.66224 (26169) hydrogen bonds : bond 0.03192 ( 801) hydrogen bonds : angle 4.58664 ( 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 420 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 358 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7251 (m-70) cc_final: 0.6522 (m170) REVERT: A 369 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6840 (mt-10) REVERT: A 445 HIS cc_start: 0.8412 (m-70) cc_final: 0.8079 (m-70) REVERT: A 462 LEU cc_start: 0.9048 (mt) cc_final: 0.8705 (mp) REVERT: A 539 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: A 607 LYS cc_start: 0.7713 (pptt) cc_final: 0.7490 (ptmt) REVERT: A 680 TYR cc_start: 0.8383 (t80) cc_final: 0.8127 (t80) REVERT: A 701 VAL cc_start: 0.9326 (t) cc_final: 0.9043 (p) REVERT: B 419 GLN cc_start: 0.7558 (tt0) cc_final: 0.6814 (mt0) REVERT: B 441 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8356 (mm) REVERT: B 540 ARG cc_start: 0.7698 (mtm180) cc_final: 0.6822 (mmt-90) REVERT: B 680 TYR cc_start: 0.8175 (t80) cc_final: 0.7751 (t80) REVERT: C 455 ASP cc_start: 0.8184 (t0) cc_final: 0.7793 (t0) REVERT: C 484 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9112 (mm) REVERT: C 650 ILE cc_start: 0.9455 (mm) cc_final: 0.9228 (mt) REVERT: C 706 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7179 (pt0) REVERT: D 434 GLU cc_start: 0.7048 (tp30) cc_final: 0.6780 (tp30) REVERT: D 547 VAL cc_start: 0.8371 (t) cc_final: 0.8073 (p) REVERT: D 555 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8259 (ptp-170) REVERT: D 632 ARG cc_start: 0.7952 (mtm180) cc_final: 0.7600 (mtm-85) REVERT: D 657 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8210 (ttmt) REVERT: D 659 ASP cc_start: 0.7547 (m-30) cc_final: 0.7293 (m-30) REVERT: D 661 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7443 (ptp-110) REVERT: D 662 THR cc_start: 0.8575 (m) cc_final: 0.8191 (p) REVERT: D 719 ASP cc_start: 0.6691 (t0) cc_final: 0.6306 (t70) REVERT: E 631 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8278 (mm-40) REVERT: F 675 HIS cc_start: 0.6593 (m-70) cc_final: 0.5752 (m-70) outliers start: 62 outliers final: 46 residues processed: 395 average time/residue: 0.1202 time to fit residues: 76.7681 Evaluate side-chains 392 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 343 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 441 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 539 TYR 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 A residue 666 GLN Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 678 MET 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 454 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 488 THR 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 407 THR Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 593 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 86 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 161 optimal weight: 0.6980 chunk 189 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS F 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.097610 restraints weight = 36164.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099863 restraints weight = 23505.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100585 restraints weight = 18445.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102180 restraints weight = 14461.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102194 restraints weight = 12201.635| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4641 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= 0.134 Angle : 0.693 14.528 26169 Z= 0.328 Chirality : 0.046 0.170 3128 Planarity : 0.004 0.042 3227 Dihedral : 13.028 158.102 2908 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.74 % Allowed : 20.84 % Favored : 76.42 % 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: -0.18 (0.18), residues: 2350 helix: 1.06 (0.18), residues: 949 sheet: -0.19 (0.26), residues: 383 loop : -1.21 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 555 TYR 0.020 0.002 TYR D 716 PHE 0.017 0.001 PHE F 597 TRP 0.019 0.002 TRP D 530 HIS 0.012 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00313 (19190) covalent geometry : angle 0.69287 (26169) hydrogen bonds : bond 0.03256 ( 801) hydrogen bonds : angle 4.61086 ( 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 404 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 360 HIS cc_start: 0.7270 (m-70) cc_final: 0.6550 (m170) REVERT: A 369 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 445 HIS cc_start: 0.8375 (m-70) cc_final: 0.8057 (m-70) REVERT: A 462 LEU cc_start: 0.9043 (mt) cc_final: 0.8670 (mp) REVERT: A 680 TYR cc_start: 0.8428 (t80) cc_final: 0.8214 (t80) REVERT: A 701 VAL cc_start: 0.9334 (t) cc_final: 0.9040 (p) REVERT: B 371 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8560 (tp40) REVERT: B 419 GLN cc_start: 0.7603 (tt0) cc_final: 0.6834 (mt0) REVERT: B 540 ARG cc_start: 0.7782 (mtm180) cc_final: 0.6775 (mtp85) REVERT: B 680 TYR cc_start: 0.8284 (t80) cc_final: 0.7817 (t80) REVERT: C 455 ASP cc_start: 0.8216 (t0) cc_final: 0.7888 (t0) REVERT: C 484 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9138 (mm) REVERT: C 520 ASP cc_start: 0.7452 (t0) cc_final: 0.7152 (t0) REVERT: C 521 MET cc_start: 0.7690 (mmt) cc_final: 0.7004 (mmt) REVERT: C 618 LYS cc_start: 0.8632 (tttt) cc_final: 0.8424 (tttt) REVERT: C 672 LEU cc_start: 0.9020 (mt) cc_final: 0.8811 (mt) REVERT: C 706 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7228 (pt0) REVERT: D 434 GLU cc_start: 0.7061 (tp30) cc_final: 0.6812 (tp30) REVERT: D 547 VAL cc_start: 0.8377 (t) cc_final: 0.8067 (p) REVERT: D 555 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8291 (ptp-170) REVERT: D 632 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7657 (mtm-85) REVERT: D 657 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8209 (ttmt) REVERT: D 659 ASP cc_start: 0.7590 (m-30) cc_final: 0.7337 (m-30) REVERT: D 661 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7418 (ptp-110) REVERT: D 662 THR cc_start: 0.8616 (m) cc_final: 0.8205 (p) REVERT: E 631 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8363 (mm-40) REVERT: F 675 HIS cc_start: 0.6737 (m-70) cc_final: 0.5947 (m-70) outliers start: 55 outliers final: 49 residues processed: 384 average time/residue: 0.1182 time to fit residues: 73.4577 Evaluate side-chains 387 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 441 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 539 TYR 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 A residue 696 VAL Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 530 TRP 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 484 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 539 TYR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 356 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 526 ASN Chi-restraints excluded: chain F residue 593 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 171 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 203 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN F 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096867 restraints weight = 36576.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099028 restraints weight = 23664.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100553 restraints weight = 17485.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.101559 restraints weight = 14111.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102310 restraints weight = 12171.400| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19190 Z= 0.134 Angle : 0.690 14.860 26169 Z= 0.325 Chirality : 0.046 0.231 3128 Planarity : 0.004 0.040 3227 Dihedral : 12.821 128.502 2908 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.94 % Allowed : 21.04 % Favored : 76.02 % 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: -0.12 (0.18), residues: 2350 helix: 1.07 (0.18), residues: 951 sheet: -0.16 (0.25), residues: 390 loop : -1.13 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 555 TYR 0.019 0.002 TYR C 432 PHE 0.025 0.001 PHE D 553 TRP 0.019 0.002 TRP C 530 HIS 0.011 0.001 HIS F 702 Details of bonding type rmsd covalent geometry : bond 0.00314 (19190) covalent geometry : angle 0.69002 (26169) hydrogen bonds : bond 0.03259 ( 801) hydrogen bonds : angle 4.60190 ( 2269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.23 seconds wall clock time: 49 minutes 42.42 seconds (2982.42 seconds total)