Starting phenix.real_space_refine on Wed Mar 20 15:29:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/03_2024/6o6r_0636.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/03_2024/6o6r_0636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/03_2024/6o6r_0636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/03_2024/6o6r_0636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/03_2024/6o6r_0636.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6r_0636/03_2024/6o6r_0636.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Na 8 4.78 5 C 18248 2.51 5 N 4484 2.21 5 O 4864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B ARG 775": "NH1" <-> "NH2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 880": "NH1" <-> "NH2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B GLU 896": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C GLU 604": "OE1" <-> "OE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C ARG 655": "NH1" <-> "NH2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 754": "OE1" <-> "OE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 880": "NH1" <-> "NH2" Residue "C GLU 883": "OE1" <-> "OE2" Residue "C GLU 896": "OE1" <-> "OE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D GLU 604": "OE1" <-> "OE2" Residue "D GLU 606": "OE1" <-> "OE2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D GLU 676": "OE1" <-> "OE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D GLU 754": "OE1" <-> "OE2" Residue "D ARG 775": "NH1" <-> "NH2" Residue "D ARG 875": "NH1" <-> "NH2" Residue "D ARG 880": "NH1" <-> "NH2" Residue "D GLU 883": "OE1" <-> "OE2" Residue "D GLU 896": "OE1" <-> "OE2" Residue "D GLU 1051": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27744 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "B" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "C" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "D" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {' NA': 2, '9PE': 1, 'LQ7': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {' NA': 2, '9PE': 1, 'LQ7': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {' NA': 2, '9PE': 1, 'LQ7': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {' NA': 2, '9PE': 1, 'LQ7': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 14.63, per 1000 atoms: 0.53 Number of scatterers: 27744 At special positions: 0 Unit cell: (128.139, 128.139, 149.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 4 15.00 Na 8 11.00 O 4864 8.00 N 4484 7.00 C 18248 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 - 3.50 Amino acid : False - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.12 Conformation dependent library (CDL) restraints added in 4.2 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6352 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 8 sheets defined 63.5% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.546A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.761A pdb=" N TYR A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.595A pdb=" N ILE A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.717A pdb=" N ARG A 359 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 360 " --> pdb=" O ILE A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 360' Processing helix chain 'A' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 375 " --> pdb=" O TRP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 395 through 409 removed outlier: 3.678A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 4.260A pdb=" N ASP A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 removed outlier: 3.852A pdb=" N ILE A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.939A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.522A pdb=" N LYS A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 626 removed outlier: 3.699A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.078A pdb=" N THR A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 removed outlier: 3.591A pdb=" N GLU A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 675 Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.767A pdb=" N ILE A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 696 Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 724 through 749 removed outlier: 3.612A pdb=" N TYR A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 775 removed outlier: 3.757A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 806 removed outlier: 3.756A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A 803 " --> pdb=" O TYR A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 removed outlier: 3.552A pdb=" N TYR A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 842 removed outlier: 3.542A pdb=" N ASP A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 879 removed outlier: 3.564A pdb=" N PHE A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 945 through 954 Processing helix chain 'A' and resid 955 through 970 removed outlier: 3.666A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.821A pdb=" N TRP A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.583A pdb=" N VAL A1006 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1059 removed outlier: 3.675A pdb=" N VAL A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A1056 " --> pdb=" O ASN A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1093 removed outlier: 3.881A pdb=" N LEU A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.546A pdb=" N SER B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.761A pdb=" N TYR B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.596A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.716A pdb=" N ARG B 359 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 360' Processing helix chain 'B' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 375 " --> pdb=" O TRP B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.679A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 4.261A pdb=" N ASP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 493 through 507 Processing helix chain 'B' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 562 removed outlier: 3.852A pdb=" N ILE B 557 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.938A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.521A pdb=" N LYS B 590 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 626 removed outlier: 3.698A pdb=" N GLU B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.077A pdb=" N THR B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 653 removed outlier: 3.592A pdb=" N GLU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 683 through 692 removed outlier: 3.767A pdb=" N ILE B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 690 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 696 Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.613A pdb=" N TYR B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 775 removed outlier: 3.757A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 806 removed outlier: 3.756A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 803 " --> pdb=" O TYR B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 816 removed outlier: 3.553A pdb=" N TYR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 842 removed outlier: 3.543A pdb=" N ASP B 825 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 879 removed outlier: 3.563A pdb=" N PHE B 859 " --> pdb=" O ILE B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 945 through 954 Processing helix chain 'B' and resid 955 through 970 removed outlier: 3.666A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.822A pdb=" N TRP B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1006 removed outlier: 3.583A pdb=" N VAL B1006 " --> pdb=" O PHE B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1059 removed outlier: 3.675A pdb=" N VAL B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B1056 " --> pdb=" O ASN B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1093 removed outlier: 3.881A pdb=" N LEU B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B1090 " --> pdb=" O LEU B1086 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.546A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.760A pdb=" N TYR C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.595A pdb=" N ILE C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 343 through 348 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.717A pdb=" N ARG C 359 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 360 " --> pdb=" O ILE C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 375 " --> pdb=" O TRP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 395 through 409 removed outlier: 3.678A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 4.261A pdb=" N ASP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 493 through 507 Processing helix chain 'C' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 562 removed outlier: 3.851A pdb=" N ILE C 557 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.938A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.521A pdb=" N LYS C 590 " --> pdb=" O SER C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 626 removed outlier: 3.700A pdb=" N GLU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 4.078A pdb=" N THR C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 653 removed outlier: 3.591A pdb=" N GLU C 653 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 675 Processing helix chain 'C' and resid 683 through 692 removed outlier: 3.767A pdb=" N ILE C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 690 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 696 Processing helix chain 'C' and resid 717 through 722 Processing helix chain 'C' and resid 724 through 749 removed outlier: 3.612A pdb=" N TYR C 745 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 775 removed outlier: 3.757A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 806 removed outlier: 3.756A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 802 " --> pdb=" O PHE C 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 803 " --> pdb=" O TYR C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 816 removed outlier: 3.553A pdb=" N TYR C 816 " --> pdb=" O GLU C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 842 removed outlier: 3.542A pdb=" N ASP C 825 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 879 removed outlier: 3.563A pdb=" N PHE C 859 " --> pdb=" O ILE C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 893 Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 945 through 954 Processing helix chain 'C' and resid 955 through 970 removed outlier: 3.666A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.821A pdb=" N TRP C 984 " --> pdb=" O ASN C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1006 removed outlier: 3.583A pdb=" N VAL C1006 " --> pdb=" O PHE C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1059 removed outlier: 3.675A pdb=" N VAL C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C1056 " --> pdb=" O ASN C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1093 removed outlier: 3.881A pdb=" N LEU C1085 " --> pdb=" O ASP C1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C1090 " --> pdb=" O LEU C1086 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 151 through 167 removed outlier: 3.545A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.760A pdb=" N TYR D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 removed outlier: 3.595A pdb=" N ILE D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 343 through 348 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.718A pdb=" N ARG D 359 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 360 " --> pdb=" O ILE D 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 360' Processing helix chain 'D' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 375 " --> pdb=" O TRP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 395 through 409 removed outlier: 3.677A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 removed outlier: 4.260A pdb=" N ASP D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 493 through 507 Processing helix chain 'D' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE D 514 " --> pdb=" O ALA D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 562 removed outlier: 3.852A pdb=" N ILE D 557 " --> pdb=" O GLN D 553 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 573 removed outlier: 3.939A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 removed outlier: 3.521A pdb=" N LYS D 590 " --> pdb=" O SER D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 626 removed outlier: 3.700A pdb=" N GLU D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 4.078A pdb=" N THR D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 653 removed outlier: 3.592A pdb=" N GLU D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 675 Processing helix chain 'D' and resid 683 through 692 removed outlier: 3.766A pdb=" N ILE D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 690 " --> pdb=" O ILE D 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 696 Processing helix chain 'D' and resid 717 through 722 Processing helix chain 'D' and resid 724 through 749 removed outlier: 3.613A pdb=" N TYR D 745 " --> pdb=" O LEU D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 775 removed outlier: 3.758A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 806 removed outlier: 3.757A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 797 " --> pdb=" O ASP D 793 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 802 " --> pdb=" O PHE D 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 803 " --> pdb=" O TYR D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 816 removed outlier: 3.553A pdb=" N TYR D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 842 removed outlier: 3.542A pdb=" N ASP D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 879 removed outlier: 3.564A pdb=" N PHE D 859 " --> pdb=" O ILE D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 893 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 955 through 970 removed outlier: 3.667A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 997 removed outlier: 3.821A pdb=" N TRP D 984 " --> pdb=" O ASN D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1006 removed outlier: 3.582A pdb=" N VAL D1006 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 3.676A pdb=" N VAL D1048 " --> pdb=" O ALA D1044 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D1056 " --> pdb=" O ASN D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1093 removed outlier: 3.882A pdb=" N LEU D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.037A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP A 169 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 292 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.036A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP B 169 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 292 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.037A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP C 169 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 292 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 107 through 108 removed outlier: 6.037A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP D 169 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 292 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 11.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4332 1.31 - 1.43: 7953 1.43 - 1.56: 15822 1.56 - 1.69: 49 1.69 - 1.82: 220 Bond restraints: 28376 Sorted by residual: bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.25e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.23e+02 bond pdb=" CBF Y01 D1301 " pdb=" CBH Y01 D1301 " ideal model delta sigma weight residual 1.550 1.716 -0.166 2.00e-02 2.50e+03 6.86e+01 ... (remaining 28371 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.52: 388 105.52 - 112.72: 14741 112.72 - 119.93: 10805 119.93 - 127.13: 12025 127.13 - 134.34: 365 Bond angle restraints: 38324 Sorted by residual: angle pdb=" C THR C 681 " pdb=" N LYS C 682 " pdb=" CA LYS C 682 " ideal model delta sigma weight residual 121.54 132.49 -10.95 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C THR A 681 " pdb=" N LYS A 682 " pdb=" CA LYS A 682 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" C THR D 681 " pdb=" N LYS D 682 " pdb=" CA LYS D 682 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 angle pdb=" C THR B 681 " pdb=" N LYS B 682 " pdb=" CA LYS B 682 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" N PHE B1003 " pdb=" CA PHE B1003 " pdb=" C PHE B1003 " ideal model delta sigma weight residual 113.16 120.14 -6.98 1.42e+00 4.96e-01 2.42e+01 ... (remaining 38319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 16412 34.45 - 68.90: 464 68.90 - 103.35: 40 103.35 - 137.80: 4 137.80 - 172.25: 4 Dihedral angle restraints: 16924 sinusoidal: 7156 harmonic: 9768 Sorted by residual: dihedral pdb=" CA ILE B 315 " pdb=" C ILE B 315 " pdb=" N PRO B 316 " pdb=" CA PRO B 316 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE D 315 " pdb=" C ILE D 315 " pdb=" N PRO D 316 " pdb=" CA PRO D 316 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE A 315 " pdb=" C ILE A 315 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 16921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4001 0.096 - 0.191: 239 0.191 - 0.287: 18 0.287 - 0.382: 6 0.382 - 0.478: 4 Chirality restraints: 4268 Sorted by residual: chirality pdb=" CBI Y01 C1301 " pdb=" CAU Y01 C1301 " pdb=" CBE Y01 C1301 " pdb=" CBG Y01 C1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CBI Y01 A1301 " pdb=" CAU Y01 A1301 " pdb=" CBE Y01 A1301 " pdb=" CBG Y01 A1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CBI Y01 D1301 " pdb=" CAU Y01 D1301 " pdb=" CBE Y01 D1301 " pdb=" CBG Y01 D1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 4265 not shown) Planarity restraints: 4684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 132 " -0.047 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO D 133 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO A 133 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 132 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO B 133 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.040 5.00e-02 4.00e+02 ... (remaining 4681 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 448 2.67 - 3.23: 25582 3.23 - 3.79: 43144 3.79 - 4.34: 60724 4.34 - 4.90: 95861 Nonbonded interactions: 225759 Sorted by model distance: nonbonded pdb=" CG2 VAL C 768 " pdb=" CZ PHE C1003 " model vdw 2.114 3.760 nonbonded pdb=" CG2 VAL A 768 " pdb=" CZ PHE A1003 " model vdw 2.115 3.760 nonbonded pdb=" CG2 VAL B 768 " pdb=" CZ PHE B1003 " model vdw 2.115 3.760 nonbonded pdb=" CG2 VAL D 768 " pdb=" CZ PHE D1003 " model vdw 2.115 3.760 nonbonded pdb=" CD1 LEU D 769 " pdb=" CZ PHE D1003 " model vdw 2.177 3.760 ... (remaining 225754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 1.720 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: 0.020 Extract box with map and model: 8.040 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 69.630 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.010 0.360 28376 Z= 0.595 Angle : 1.006 12.498 38324 Z= 0.502 Chirality : 0.057 0.478 4268 Planarity : 0.007 0.072 4684 Dihedral : 16.654 172.252 10572 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.54 (0.09), residues: 3252 helix: -4.46 (0.04), residues: 2176 sheet: -2.72 (0.36), residues: 180 loop : -3.55 (0.16), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 886 HIS 0.004 0.001 HIS B 176 PHE 0.042 0.002 PHE D 295 TYR 0.020 0.002 TYR B 995 ARG 0.004 0.001 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 710 time to evaluate : 2.957 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 108 TYR cc_start: 0.6950 (p90) cc_final: 0.6563 (p90) REVERT: A 181 LYS cc_start: 0.8816 (ptmm) cc_final: 0.8557 (tttt) REVERT: A 267 LYS cc_start: 0.8383 (tttp) cc_final: 0.7939 (ttmm) REVERT: A 271 GLN cc_start: 0.7347 (mt0) cc_final: 0.6693 (mt0) REVERT: A 286 TYR cc_start: 0.8664 (t80) cc_final: 0.7603 (t80) REVERT: A 304 LEU cc_start: 0.8296 (tp) cc_final: 0.8060 (tp) REVERT: A 359 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7520 (mtm110) REVERT: A 606 GLU cc_start: 0.8153 (tp30) cc_final: 0.7701 (tp30) REVERT: A 745 TYR cc_start: 0.7401 (t80) cc_final: 0.7067 (t80) REVERT: A 776 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 876 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 958 ASN cc_start: 0.9237 (t0) cc_final: 0.8967 (t0) REVERT: B 286 TYR cc_start: 0.8717 (t80) cc_final: 0.7720 (t80) REVERT: B 301 LYS cc_start: 0.8531 (tmmt) cc_final: 0.7939 (tptt) REVERT: B 328 ASP cc_start: 0.8144 (t70) cc_final: 0.7714 (t70) REVERT: B 606 GLU cc_start: 0.8197 (tp30) cc_final: 0.7812 (tp30) REVERT: B 745 TYR cc_start: 0.7289 (t80) cc_final: 0.7020 (t80) REVERT: B 776 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7759 (tm-30) REVERT: C 301 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8021 (tptt) REVERT: C 745 TYR cc_start: 0.7259 (t80) cc_final: 0.6671 (t80) REVERT: C 776 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8042 (tm-30) REVERT: D 177 TYR cc_start: 0.7504 (m-80) cc_final: 0.7140 (m-80) REVERT: D 301 LYS cc_start: 0.8257 (tmmt) cc_final: 0.7961 (tptt) REVERT: D 552 LEU cc_start: 0.9059 (mt) cc_final: 0.8833 (mt) REVERT: D 776 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7595 (tm-30) REVERT: D 876 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7362 (tm-30) outliers start: 0 outliers final: 0 residues processed: 710 average time/residue: 0.4264 time to fit residues: 465.2263 Evaluate side-chains 535 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 0.8980 chunk 251 optimal weight: 0.6980 chunk 139 optimal weight: 0.0370 chunk 85 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 chunk 301 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 271 GLN A 418 ASN A 471 ASN A 574 GLN A 597 ASN A1058 ASN ** A1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 474 ASN B 553 GLN B 574 GLN B 597 ASN B1058 ASN C 126 GLN C 248 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 474 ASN C 553 GLN C 574 GLN C 597 ASN C 610 ASN C1058 ASN D 248 HIS D 271 GLN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 574 GLN D 597 ASN D 610 ASN D 835 HIS D 958 ASN D1058 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28376 Z= 0.184 Angle : 0.614 9.484 38324 Z= 0.321 Chirality : 0.042 0.175 4268 Planarity : 0.005 0.058 4684 Dihedral : 12.010 165.854 4100 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.18 % Allowed : 15.28 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.12), residues: 3252 helix: -2.27 (0.09), residues: 2204 sheet: -2.37 (0.38), residues: 176 loop : -3.36 (0.17), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 888 HIS 0.002 0.000 HIS A 176 PHE 0.021 0.001 PHE C 497 TYR 0.019 0.001 TYR A 971 ARG 0.004 0.000 ARG A1071 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 592 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.6887 (p90) cc_final: 0.6504 (p90) REVERT: A 180 MET cc_start: 0.8207 (mtm) cc_final: 0.7991 (mtm) REVERT: A 267 LYS cc_start: 0.8174 (tttp) cc_final: 0.7754 (ttmm) REVERT: A 271 GLN cc_start: 0.7526 (mt0) cc_final: 0.6883 (mt0) REVERT: A 286 TYR cc_start: 0.8394 (t80) cc_final: 0.7428 (t80) REVERT: A 297 GLN cc_start: 0.7677 (pm20) cc_final: 0.7228 (pm20) REVERT: A 304 LEU cc_start: 0.8060 (tp) cc_final: 0.7791 (tp) REVERT: A 355 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7486 (mtm-85) REVERT: A 359 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7539 (mtt90) REVERT: A 745 TYR cc_start: 0.7554 (t80) cc_final: 0.7321 (t80) REVERT: A 771 CYS cc_start: 0.8097 (t) cc_final: 0.7870 (t) REVERT: A 776 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 876 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 286 TYR cc_start: 0.8392 (t80) cc_final: 0.7573 (t80) REVERT: B 297 GLN cc_start: 0.7884 (pm20) cc_final: 0.7414 (pm20) REVERT: B 301 LYS cc_start: 0.8345 (tmmt) cc_final: 0.7791 (tttt) REVERT: B 745 TYR cc_start: 0.7370 (t80) cc_final: 0.7163 (t80) REVERT: B 771 CYS cc_start: 0.8028 (t) cc_final: 0.7742 (t) REVERT: B 776 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 876 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 180 MET cc_start: 0.8154 (mtm) cc_final: 0.7840 (mtm) REVERT: C 286 TYR cc_start: 0.8404 (t80) cc_final: 0.7608 (t80) REVERT: C 301 LYS cc_start: 0.8446 (tmmt) cc_final: 0.7893 (tttt) REVERT: C 749 MET cc_start: 0.7455 (mmt) cc_final: 0.7155 (mmt) REVERT: C 771 CYS cc_start: 0.7928 (t) cc_final: 0.7620 (t) REVERT: C 776 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7588 (tm-30) REVERT: D 177 TYR cc_start: 0.7293 (m-80) cc_final: 0.6970 (m-80) REVERT: D 321 GLU cc_start: 0.8209 (pm20) cc_final: 0.7953 (pm20) REVERT: D 613 GLU cc_start: 0.7741 (tt0) cc_final: 0.7462 (tt0) REVERT: D 771 CYS cc_start: 0.8033 (t) cc_final: 0.7792 (t) REVERT: D 776 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 981 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7837 (t0) outliers start: 35 outliers final: 15 residues processed: 609 average time/residue: 0.3963 time to fit residues: 379.2599 Evaluate side-chains 536 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 520 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 825 ASP Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 981 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 205 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 chunk 326 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 299 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 428 ASN A 553 GLN A 790 ASN B 553 GLN B 790 ASN C 126 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN D 126 GLN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28376 Z= 0.240 Angle : 0.609 9.932 38324 Z= 0.313 Chirality : 0.042 0.175 4268 Planarity : 0.004 0.055 4684 Dihedral : 11.234 155.376 4100 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.32 % Allowed : 18.14 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.13), residues: 3252 helix: -1.10 (0.10), residues: 2196 sheet: -2.47 (0.44), residues: 140 loop : -3.23 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 371 HIS 0.003 0.001 HIS C 129 PHE 0.020 0.001 PHE C 295 TYR 0.020 0.002 TYR A 995 ARG 0.006 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 545 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7005 (p90) cc_final: 0.6566 (p90) REVERT: A 180 MET cc_start: 0.8262 (mtm) cc_final: 0.8009 (mtm) REVERT: A 286 TYR cc_start: 0.8401 (t80) cc_final: 0.7537 (t80) REVERT: A 297 GLN cc_start: 0.7732 (pm20) cc_final: 0.7531 (pm20) REVERT: A 745 TYR cc_start: 0.7587 (t80) cc_final: 0.7335 (t80) REVERT: A 771 CYS cc_start: 0.8244 (t) cc_final: 0.8012 (t) REVERT: A 776 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 825 ASP cc_start: 0.8199 (t70) cc_final: 0.7625 (t70) REVERT: B 297 GLN cc_start: 0.7792 (pm20) cc_final: 0.7416 (pm20) REVERT: B 301 LYS cc_start: 0.8399 (tmmt) cc_final: 0.7894 (tptt) REVERT: B 745 TYR cc_start: 0.7529 (t80) cc_final: 0.7324 (t80) REVERT: B 769 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7680 (mp) REVERT: B 771 CYS cc_start: 0.8198 (t) cc_final: 0.7950 (t) REVERT: B 776 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 790 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7340 (t0) REVERT: B 1046 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: C 180 MET cc_start: 0.8210 (mtm) cc_final: 0.7932 (mtm) REVERT: C 301 LYS cc_start: 0.8424 (tmmt) cc_final: 0.7912 (tptt) REVERT: C 695 LEU cc_start: 0.8746 (mt) cc_final: 0.8537 (mt) REVERT: C 700 PHE cc_start: 0.7496 (t80) cc_final: 0.7236 (t80) REVERT: C 745 TYR cc_start: 0.7386 (t80) cc_final: 0.6861 (t80) REVERT: C 771 CYS cc_start: 0.8130 (t) cc_final: 0.7815 (t) REVERT: C 776 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 177 TYR cc_start: 0.7543 (m-80) cc_final: 0.7181 (m-80) REVERT: D 305 LYS cc_start: 0.7567 (ptpp) cc_final: 0.7341 (tptp) REVERT: D 771 CYS cc_start: 0.8265 (t) cc_final: 0.8007 (t) REVERT: D 776 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8006 (tm-30) REVERT: D 825 ASP cc_start: 0.8216 (t70) cc_final: 0.7642 (t70) REVERT: D 876 GLN cc_start: 0.8077 (tp40) cc_final: 0.7638 (tm-30) REVERT: D 981 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7854 (t0) REVERT: D 1046 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8210 (pt0) outliers start: 69 outliers final: 37 residues processed: 586 average time/residue: 0.3820 time to fit residues: 355.4477 Evaluate side-chains 544 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 502 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 790 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1046 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 0.2980 chunk 227 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 320 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS A 790 ASN B 550 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN C 550 HIS C 835 HIS D 126 GLN D 471 ASN D 550 HIS D 553 GLN D 790 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28376 Z= 0.189 Angle : 0.572 10.070 38324 Z= 0.293 Chirality : 0.041 0.158 4268 Planarity : 0.004 0.052 4684 Dihedral : 10.788 153.170 4100 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.75 % Allowed : 19.95 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.14), residues: 3252 helix: -0.56 (0.11), residues: 2224 sheet: -2.25 (0.46), residues: 140 loop : -3.15 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 371 HIS 0.002 0.000 HIS A 176 PHE 0.015 0.001 PHE A 969 TYR 0.022 0.001 TYR B 286 ARG 0.006 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 546 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7142 (p90) cc_final: 0.6764 (p90) REVERT: A 180 MET cc_start: 0.8163 (mtm) cc_final: 0.7962 (mtm) REVERT: A 286 TYR cc_start: 0.8370 (t80) cc_final: 0.7570 (t80) REVERT: A 297 GLN cc_start: 0.7688 (pm20) cc_final: 0.7463 (pm20) REVERT: A 387 ILE cc_start: 0.8198 (mp) cc_final: 0.7974 (mm) REVERT: A 494 SER cc_start: 0.8599 (m) cc_final: 0.8139 (p) REVERT: A 745 TYR cc_start: 0.7554 (t80) cc_final: 0.7332 (t80) REVERT: A 776 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 790 ASN cc_start: 0.7469 (t0) cc_final: 0.7228 (t0) REVERT: B 164 GLN cc_start: 0.8334 (tp40) cc_final: 0.7722 (tp40) REVERT: B 301 LYS cc_start: 0.8407 (tmmt) cc_final: 0.7798 (tptt) REVERT: B 305 LYS cc_start: 0.8163 (ptpt) cc_final: 0.7735 (tptt) REVERT: B 494 SER cc_start: 0.8741 (m) cc_final: 0.8248 (p) REVERT: B 769 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7497 (mp) REVERT: B 776 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8365 (tm-30) REVERT: B 876 GLN cc_start: 0.8129 (tp40) cc_final: 0.7664 (tm-30) REVERT: B 1046 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: C 180 MET cc_start: 0.8185 (mtm) cc_final: 0.7811 (mtm) REVERT: C 301 LYS cc_start: 0.8382 (tmmt) cc_final: 0.7980 (tptt) REVERT: C 321 GLU cc_start: 0.8491 (pm20) cc_final: 0.8139 (pm20) REVERT: C 565 LYS cc_start: 0.8538 (tptp) cc_final: 0.8335 (tptp) REVERT: C 613 GLU cc_start: 0.7851 (tt0) cc_final: 0.7580 (tt0) REVERT: C 749 MET cc_start: 0.7641 (mmt) cc_final: 0.6974 (mmp) REVERT: C 771 CYS cc_start: 0.8173 (t) cc_final: 0.7919 (t) REVERT: C 776 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8016 (tm-30) REVERT: D 177 TYR cc_start: 0.7490 (m-80) cc_final: 0.7179 (m-80) REVERT: D 494 SER cc_start: 0.8797 (m) cc_final: 0.8259 (p) REVERT: D 553 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: D 771 CYS cc_start: 0.8236 (t) cc_final: 0.8021 (t) REVERT: D 776 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7949 (tm-30) REVERT: D 876 GLN cc_start: 0.8109 (tp40) cc_final: 0.7623 (tm-30) REVERT: D 981 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7837 (t0) REVERT: D 1046 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8201 (pt0) outliers start: 52 outliers final: 27 residues processed: 577 average time/residue: 0.3895 time to fit residues: 356.1116 Evaluate side-chains 530 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 498 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 767 PHE Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1046 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 474 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN D 126 GLN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28376 Z= 0.287 Angle : 0.611 10.965 38324 Z= 0.313 Chirality : 0.043 0.172 4268 Planarity : 0.004 0.049 4684 Dihedral : 10.760 152.699 4100 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.46 % Allowed : 20.79 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3252 helix: -0.40 (0.11), residues: 2224 sheet: -2.33 (0.46), residues: 140 loop : -3.10 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 371 HIS 0.003 0.001 HIS C 412 PHE 0.020 0.001 PHE B 295 TYR 0.025 0.002 TYR D 286 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 521 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7217 (p90) cc_final: 0.6791 (p90) REVERT: A 494 SER cc_start: 0.8645 (m) cc_final: 0.8188 (p) REVERT: A 745 TYR cc_start: 0.7594 (t80) cc_final: 0.7358 (t80) REVERT: A 776 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 825 ASP cc_start: 0.8205 (t70) cc_final: 0.7598 (t70) REVERT: A 876 GLN cc_start: 0.8137 (tp40) cc_final: 0.7638 (tm-30) REVERT: B 164 GLN cc_start: 0.8305 (tp40) cc_final: 0.7572 (tt0) REVERT: B 301 LYS cc_start: 0.8513 (tmmt) cc_final: 0.7874 (tptt) REVERT: B 305 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7796 (tptt) REVERT: B 494 SER cc_start: 0.8727 (m) cc_final: 0.8248 (p) REVERT: B 745 TYR cc_start: 0.7563 (t80) cc_final: 0.7362 (t80) REVERT: B 776 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 777 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: B 790 ASN cc_start: 0.7409 (t0) cc_final: 0.7075 (t0) REVERT: B 876 GLN cc_start: 0.8151 (tp40) cc_final: 0.7704 (tm-30) REVERT: C 180 MET cc_start: 0.8171 (mtm) cc_final: 0.7871 (mtm) REVERT: C 301 LYS cc_start: 0.8442 (tmmt) cc_final: 0.7955 (tptt) REVERT: C 494 SER cc_start: 0.8818 (m) cc_final: 0.8347 (p) REVERT: C 553 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: C 613 GLU cc_start: 0.7934 (tt0) cc_final: 0.7601 (tt0) REVERT: C 745 TYR cc_start: 0.7519 (t80) cc_final: 0.7306 (t80) REVERT: C 771 CYS cc_start: 0.8287 (t) cc_final: 0.8045 (t) REVERT: C 776 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 777 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: C 790 ASN cc_start: 0.7119 (t0) cc_final: 0.6667 (t0) REVERT: C 876 GLN cc_start: 0.8139 (tp40) cc_final: 0.7888 (tm-30) REVERT: C 1068 MET cc_start: 0.4638 (mpp) cc_final: 0.4412 (mtp) REVERT: C 1085 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4914 (tt) REVERT: C 1086 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4856 (mp) REVERT: D 177 TYR cc_start: 0.7649 (m-80) cc_final: 0.7423 (m-80) REVERT: D 494 SER cc_start: 0.8781 (m) cc_final: 0.8268 (p) REVERT: D 613 GLU cc_start: 0.7761 (tt0) cc_final: 0.7531 (tt0) REVERT: D 771 CYS cc_start: 0.8329 (t) cc_final: 0.8098 (t) REVERT: D 776 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7652 (tm-30) REVERT: D 784 TYR cc_start: 0.7458 (t80) cc_final: 0.6831 (t80) REVERT: D 825 ASP cc_start: 0.8303 (t70) cc_final: 0.7686 (t70) REVERT: D 876 GLN cc_start: 0.8205 (tp40) cc_final: 0.7663 (tm-30) outliers start: 73 outliers final: 55 residues processed: 566 average time/residue: 0.3935 time to fit residues: 352.7622 Evaluate side-chains 556 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 496 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 777 TRP Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 849 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 0.0050 chunk 321 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.0470 chunk 168 optimal weight: 0.9980 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 474 ASN D 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28376 Z= 0.169 Angle : 0.550 9.810 38324 Z= 0.284 Chirality : 0.041 0.189 4268 Planarity : 0.004 0.050 4684 Dihedral : 10.395 151.085 4100 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.39 % Allowed : 21.74 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 3252 helix: -0.04 (0.11), residues: 2192 sheet: -2.07 (0.47), residues: 140 loop : -3.04 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 371 HIS 0.002 0.000 HIS B1070 PHE 0.021 0.001 PHE D 146 TYR 0.026 0.001 TYR B 784 ARG 0.005 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 561 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7315 (p90) cc_final: 0.6950 (p90) REVERT: A 164 GLN cc_start: 0.8257 (tp40) cc_final: 0.7543 (tt0) REVERT: A 494 SER cc_start: 0.8749 (m) cc_final: 0.8304 (p) REVERT: A 773 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8196 (mm-30) REVERT: A 776 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 876 GLN cc_start: 0.8071 (tp40) cc_final: 0.7575 (tm-30) REVERT: B 164 GLN cc_start: 0.8350 (tp40) cc_final: 0.7606 (tt0) REVERT: B 301 LYS cc_start: 0.8493 (tmmt) cc_final: 0.7782 (tptt) REVERT: B 305 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7759 (tptt) REVERT: B 494 SER cc_start: 0.8812 (m) cc_final: 0.8327 (p) REVERT: B 776 GLN cc_start: 0.8598 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 876 GLN cc_start: 0.8144 (tp40) cc_final: 0.7797 (tm-30) REVERT: B 1075 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7406 (tt) REVERT: C 180 MET cc_start: 0.8168 (mtm) cc_final: 0.7924 (mtm) REVERT: C 301 LYS cc_start: 0.8409 (tmmt) cc_final: 0.7810 (tptt) REVERT: C 305 LYS cc_start: 0.7879 (ptmt) cc_final: 0.7659 (tptt) REVERT: C 321 GLU cc_start: 0.8493 (pm20) cc_final: 0.8143 (pm20) REVERT: C 363 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7774 (mm-30) REVERT: C 494 SER cc_start: 0.8764 (m) cc_final: 0.8287 (p) REVERT: C 613 GLU cc_start: 0.7783 (tt0) cc_final: 0.7471 (tt0) REVERT: C 771 CYS cc_start: 0.8346 (t) cc_final: 0.8114 (t) REVERT: C 776 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 777 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: C 876 GLN cc_start: 0.8133 (tp40) cc_final: 0.7853 (tm-30) REVERT: C 969 PHE cc_start: 0.8462 (m-80) cc_final: 0.8255 (m-80) REVERT: D 494 SER cc_start: 0.8745 (m) cc_final: 0.8234 (p) REVERT: D 516 TRP cc_start: 0.7201 (t-100) cc_final: 0.6971 (t60) REVERT: D 613 GLU cc_start: 0.7750 (tt0) cc_final: 0.7502 (tt0) REVERT: D 771 CYS cc_start: 0.8301 (t) cc_final: 0.8093 (t) REVERT: D 776 GLN cc_start: 0.8443 (tm-30) cc_final: 0.7969 (tm-30) REVERT: D 1075 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7090 (tt) outliers start: 71 outliers final: 49 residues processed: 613 average time/residue: 0.3967 time to fit residues: 381.4519 Evaluate side-chains 572 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 519 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 700 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 183 optimal weight: 0.0370 chunk 234 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 319 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 412 HIS C 550 HIS D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28376 Z= 0.185 Angle : 0.558 9.751 38324 Z= 0.287 Chirality : 0.041 0.188 4268 Planarity : 0.004 0.049 4684 Dihedral : 10.252 151.349 4100 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.83 % Allowed : 21.53 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 3252 helix: 0.10 (0.11), residues: 2164 sheet: -1.98 (0.47), residues: 140 loop : -2.85 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 371 HIS 0.002 0.000 HIS D1070 PHE 0.016 0.001 PHE D 146 TYR 0.026 0.001 TYR B 784 ARG 0.003 0.000 ARG D 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 548 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7341 (p90) cc_final: 0.6929 (p90) REVERT: A 164 GLN cc_start: 0.8294 (tp40) cc_final: 0.7543 (tt0) REVERT: A 301 LYS cc_start: 0.8499 (tmmt) cc_final: 0.7897 (tptt) REVERT: A 494 SER cc_start: 0.8716 (m) cc_final: 0.8256 (p) REVERT: A 606 GLU cc_start: 0.8044 (tp30) cc_final: 0.7648 (tp30) REVERT: A 777 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.7511 (m-10) REVERT: B 164 GLN cc_start: 0.8350 (tp40) cc_final: 0.7566 (tt0) REVERT: B 301 LYS cc_start: 0.8397 (tmmt) cc_final: 0.7743 (tptt) REVERT: B 305 LYS cc_start: 0.8077 (ptpt) cc_final: 0.7741 (tptt) REVERT: B 494 SER cc_start: 0.8785 (m) cc_final: 0.8302 (p) REVERT: B 773 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 776 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 876 GLN cc_start: 0.8092 (tp40) cc_final: 0.7720 (tm-30) REVERT: B 953 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6264 (t80) REVERT: B 1075 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7337 (tt) REVERT: C 180 MET cc_start: 0.8201 (mtm) cc_final: 0.7980 (mtm) REVERT: C 301 LYS cc_start: 0.8406 (tmmt) cc_final: 0.7795 (tptt) REVERT: C 305 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7682 (tptt) REVERT: C 321 GLU cc_start: 0.8477 (pm20) cc_final: 0.8234 (pm20) REVERT: C 363 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: C 494 SER cc_start: 0.8747 (m) cc_final: 0.8270 (p) REVERT: C 613 GLU cc_start: 0.7835 (tt0) cc_final: 0.7540 (tt0) REVERT: C 771 CYS cc_start: 0.8375 (t) cc_final: 0.8170 (t) REVERT: C 776 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 777 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: C 1085 LEU cc_start: 0.5135 (OUTLIER) cc_final: 0.4841 (tt) REVERT: D 494 SER cc_start: 0.8696 (m) cc_final: 0.8194 (p) REVERT: D 516 TRP cc_start: 0.7197 (t-100) cc_final: 0.6707 (t60) REVERT: D 613 GLU cc_start: 0.7771 (tt0) cc_final: 0.7523 (tt0) REVERT: D 776 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7691 (tm-30) REVERT: D 784 TYR cc_start: 0.7538 (t80) cc_final: 0.7059 (t80) REVERT: D 876 GLN cc_start: 0.8104 (tp40) cc_final: 0.7581 (tm-30) REVERT: D 1075 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7115 (tt) outliers start: 84 outliers final: 54 residues processed: 604 average time/residue: 0.3890 time to fit residues: 370.1744 Evaluate side-chains 590 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 529 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 777 TRP Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 428 ASN Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 550 HIS D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28376 Z= 0.233 Angle : 0.584 9.669 38324 Z= 0.300 Chirality : 0.042 0.176 4268 Planarity : 0.004 0.048 4684 Dihedral : 10.268 151.172 4100 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.59 % Allowed : 21.90 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3252 helix: 0.11 (0.11), residues: 2172 sheet: -2.02 (0.47), residues: 140 loop : -2.87 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 684 HIS 0.004 0.001 HIS C 412 PHE 0.016 0.001 PHE D 146 TYR 0.035 0.002 TYR D 286 ARG 0.004 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 530 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7412 (p90) cc_final: 0.6988 (p90) REVERT: A 301 LYS cc_start: 0.8552 (tmmt) cc_final: 0.7958 (tptt) REVERT: A 387 ILE cc_start: 0.8136 (mp) cc_final: 0.7769 (mt) REVERT: A 494 SER cc_start: 0.8759 (m) cc_final: 0.8301 (p) REVERT: A 777 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.7543 (m-10) REVERT: A 876 GLN cc_start: 0.8084 (tp40) cc_final: 0.7594 (tm-30) REVERT: B 164 GLN cc_start: 0.8379 (tp40) cc_final: 0.7564 (tt0) REVERT: B 301 LYS cc_start: 0.8409 (tmmt) cc_final: 0.7753 (tptt) REVERT: B 305 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7769 (tptt) REVERT: B 494 SER cc_start: 0.8806 (m) cc_final: 0.8323 (p) REVERT: B 773 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8188 (mm-30) REVERT: B 776 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 876 GLN cc_start: 0.8172 (tp40) cc_final: 0.7774 (tm-30) REVERT: B 1068 MET cc_start: 0.6345 (tpt) cc_final: 0.5400 (pmm) REVERT: B 1075 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7518 (mp) REVERT: C 180 MET cc_start: 0.8188 (mtm) cc_final: 0.7983 (mtm) REVERT: C 301 LYS cc_start: 0.8382 (tmmt) cc_final: 0.7853 (tptt) REVERT: C 321 GLU cc_start: 0.8503 (pm20) cc_final: 0.8145 (pm20) REVERT: C 494 SER cc_start: 0.8757 (m) cc_final: 0.8269 (p) REVERT: C 613 GLU cc_start: 0.7833 (tt0) cc_final: 0.7512 (tt0) REVERT: C 777 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: C 876 GLN cc_start: 0.8108 (tp40) cc_final: 0.7640 (tm-30) REVERT: C 1085 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4742 (tt) REVERT: D 494 SER cc_start: 0.8706 (m) cc_final: 0.8212 (p) REVERT: D 516 TRP cc_start: 0.7272 (t-100) cc_final: 0.6732 (t60) REVERT: D 613 GLU cc_start: 0.7712 (tt0) cc_final: 0.7481 (tt0) REVERT: D 685 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8646 (tttp) REVERT: D 776 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7613 (tm-30) REVERT: D 825 ASP cc_start: 0.8177 (t70) cc_final: 0.7950 (m-30) REVERT: D 876 GLN cc_start: 0.8164 (tp40) cc_final: 0.7626 (tm-30) REVERT: D 1075 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7119 (tt) outliers start: 77 outliers final: 63 residues processed: 579 average time/residue: 0.3953 time to fit residues: 361.4863 Evaluate side-chains 580 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 511 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 777 TRP Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 298 optimal weight: 0.4980 chunk 179 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 234 optimal weight: 0.9980 chunk 91 optimal weight: 0.0050 chunk 269 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 412 HIS C 550 HIS D 126 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28376 Z= 0.166 Angle : 0.565 9.357 38324 Z= 0.291 Chirality : 0.041 0.151 4268 Planarity : 0.004 0.049 4684 Dihedral : 10.102 150.243 4100 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.29 % Allowed : 22.24 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3252 helix: 0.28 (0.11), residues: 2164 sheet: -1.93 (0.48), residues: 136 loop : -2.81 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 684 HIS 0.007 0.001 HIS B1070 PHE 0.018 0.001 PHE C 858 TYR 0.040 0.001 TYR C 286 ARG 0.008 0.000 ARG B1071 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 541 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7398 (p90) cc_final: 0.6941 (p90) REVERT: A 164 GLN cc_start: 0.8307 (tp40) cc_final: 0.7551 (tt0) REVERT: A 301 LYS cc_start: 0.8549 (tmmt) cc_final: 0.7920 (tptt) REVERT: A 387 ILE cc_start: 0.8170 (mp) cc_final: 0.7808 (mt) REVERT: A 494 SER cc_start: 0.8702 (m) cc_final: 0.8235 (p) REVERT: B 130 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8473 (pp) REVERT: B 164 GLN cc_start: 0.8362 (tp40) cc_final: 0.7577 (tt0) REVERT: B 301 LYS cc_start: 0.8421 (tmmt) cc_final: 0.7749 (tptt) REVERT: B 305 LYS cc_start: 0.8058 (ptpt) cc_final: 0.7729 (tptt) REVERT: B 387 ILE cc_start: 0.8103 (mp) cc_final: 0.7881 (mm) REVERT: B 494 SER cc_start: 0.8752 (m) cc_final: 0.8274 (p) REVERT: B 773 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8204 (mm-30) REVERT: B 776 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 953 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6305 (t80) REVERT: B 1075 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7495 (mp) REVERT: C 301 LYS cc_start: 0.8441 (tmmt) cc_final: 0.7985 (tptt) REVERT: C 321 GLU cc_start: 0.8437 (pm20) cc_final: 0.8227 (pm20) REVERT: C 494 SER cc_start: 0.8828 (m) cc_final: 0.8335 (p) REVERT: C 613 GLU cc_start: 0.7770 (tt0) cc_final: 0.7472 (tt0) REVERT: C 771 CYS cc_start: 0.8389 (t) cc_final: 0.8166 (t) REVERT: C 876 GLN cc_start: 0.8034 (tp40) cc_final: 0.7738 (tm-30) REVERT: C 1085 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4752 (tt) REVERT: D 494 SER cc_start: 0.8788 (m) cc_final: 0.8291 (p) REVERT: D 516 TRP cc_start: 0.7213 (t-100) cc_final: 0.6738 (t60) REVERT: D 613 GLU cc_start: 0.7721 (tt0) cc_final: 0.7463 (tt0) REVERT: D 776 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 1075 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7381 (mp) outliers start: 68 outliers final: 54 residues processed: 588 average time/residue: 0.3871 time to fit residues: 360.6662 Evaluate side-chains 569 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 510 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 2.9990 chunk 315 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 chunk 330 optimal weight: 0.7980 chunk 304 optimal weight: 0.6980 chunk 263 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 203 optimal weight: 0.0770 chunk 161 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 412 HIS C 410 ASN C 550 HIS D 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28376 Z= 0.172 Angle : 0.575 9.860 38324 Z= 0.295 Chirality : 0.041 0.215 4268 Planarity : 0.004 0.051 4684 Dihedral : 10.004 150.044 4100 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.09 % Allowed : 22.68 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3252 helix: 0.35 (0.11), residues: 2188 sheet: -1.88 (0.48), residues: 136 loop : -2.80 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 684 HIS 0.002 0.000 HIS B 129 PHE 0.024 0.001 PHE B 700 TYR 0.051 0.002 TYR B 286 ARG 0.004 0.000 ARG D1071 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 529 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7366 (p90) cc_final: 0.7002 (p90) REVERT: A 164 GLN cc_start: 0.8300 (tp40) cc_final: 0.7559 (tt0) REVERT: A 267 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8036 (tmtt) REVERT: A 301 LYS cc_start: 0.8475 (tmmt) cc_final: 0.7780 (tptt) REVERT: A 305 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7885 (tptt) REVERT: A 387 ILE cc_start: 0.8166 (mp) cc_final: 0.7804 (mt) REVERT: A 494 SER cc_start: 0.8688 (m) cc_final: 0.8223 (p) REVERT: B 164 GLN cc_start: 0.8358 (tp40) cc_final: 0.7568 (tt0) REVERT: B 301 LYS cc_start: 0.8409 (tmmt) cc_final: 0.7680 (tptt) REVERT: B 305 LYS cc_start: 0.8045 (ptpt) cc_final: 0.7722 (tptt) REVERT: B 387 ILE cc_start: 0.8117 (mp) cc_final: 0.7898 (mm) REVERT: B 494 SER cc_start: 0.8732 (m) cc_final: 0.8271 (p) REVERT: B 876 GLN cc_start: 0.8075 (tp40) cc_final: 0.7587 (tm-30) REVERT: B 954 MET cc_start: 0.8420 (mmp) cc_final: 0.8016 (mtp) REVERT: B 1075 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7477 (mp) REVERT: C 301 LYS cc_start: 0.8520 (tmmt) cc_final: 0.7932 (tptt) REVERT: C 321 GLU cc_start: 0.8401 (pm20) cc_final: 0.8199 (pm20) REVERT: C 494 SER cc_start: 0.8810 (m) cc_final: 0.8333 (p) REVERT: C 613 GLU cc_start: 0.7765 (tt0) cc_final: 0.7459 (tt0) REVERT: C 1068 MET cc_start: 0.5246 (tpp) cc_final: 0.4971 (tpp) REVERT: C 1085 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4722 (tt) REVERT: D 494 SER cc_start: 0.8772 (m) cc_final: 0.8290 (p) REVERT: D 516 TRP cc_start: 0.7181 (t-100) cc_final: 0.6630 (t60) REVERT: D 613 GLU cc_start: 0.7692 (tt0) cc_final: 0.7438 (tt0) REVERT: D 776 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8171 (tm-30) REVERT: D 876 GLN cc_start: 0.8043 (tp40) cc_final: 0.7546 (tm-30) REVERT: D 1075 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7416 (mp) outliers start: 62 outliers final: 55 residues processed: 575 average time/residue: 0.4129 time to fit residues: 378.3839 Evaluate side-chains 567 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 509 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1068 MET Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 263 optimal weight: 0.0470 chunk 110 optimal weight: 0.7980 chunk 270 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 412 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS D 126 GLN ** D 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.173618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129233 restraints weight = 34201.472| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.53 r_work: 0.3208 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28376 Z= 0.175 Angle : 0.576 9.567 38324 Z= 0.294 Chirality : 0.041 0.223 4268 Planarity : 0.004 0.049 4684 Dihedral : 9.889 149.846 4100 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.09 % Allowed : 22.75 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3252 helix: 0.43 (0.11), residues: 2188 sheet: -1.79 (0.48), residues: 136 loop : -2.77 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 684 HIS 0.002 0.000 HIS B 129 PHE 0.016 0.001 PHE C 858 TYR 0.048 0.001 TYR D 286 ARG 0.003 0.000 ARG B1071 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7143.40 seconds wall clock time: 128 minutes 56.64 seconds (7736.64 seconds total)