Starting phenix.real_space_refine on Tue Dec 31 20:49:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv0_35735/12_2024/8iv0_35735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv0_35735/12_2024/8iv0_35735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv0_35735/12_2024/8iv0_35735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv0_35735/12_2024/8iv0_35735.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv0_35735/12_2024/8iv0_35735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv0_35735/12_2024/8iv0_35735.cif" } resolution = 2.9 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= 0.017 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10386 2.51 5 N 2919 2.21 5 O 3306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16701 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 904 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 10.11, per 1000 atoms: 0.61 Number of scatterers: 16701 At special positions: 0 Unit cell: (115.132, 121.588, 175.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3306 8.00 N 2919 7.00 C 10386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 48 sheets defined 18.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.789A pdb=" N THR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 4.059A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.822A pdb=" N ARG A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 400 through 450 removed outlier: 5.010A pdb=" N GLU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.084A pdb=" N MET A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.546A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.890A pdb=" N LYS B 66 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 67' Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.587A pdb=" N SER B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.556A pdb=" N ASP C 86 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.788A pdb=" N THR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 4.059A pdb=" N LEU D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 106 removed outlier: 4.822A pdb=" N ARG D 104 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 400 through 450 removed outlier: 5.010A pdb=" N GLU D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG D 447 " --> pdb=" O LYS D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.085A pdb=" N MET D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 removed outlier: 3.547A pdb=" N MET D 493 " --> pdb=" O ARG D 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.890A pdb=" N LYS E 66 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA E 67 " --> pdb=" O LYS E 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 67' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.587A pdb=" N SER E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.557A pdb=" N ASP F 86 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 87 " --> pdb=" O GLU F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 87' Processing helix chain 'G' and resid 58 through 63 removed outlier: 3.788A pdb=" N THR G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 4.059A pdb=" N LEU G 71 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 100 Processing helix chain 'G' and resid 101 through 106 removed outlier: 4.821A pdb=" N ARG G 104 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 382 Processing helix chain 'G' and resid 400 through 450 removed outlier: 5.010A pdb=" N GLU G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET G 441 " --> pdb=" O ALA G 437 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP G 442 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG G 447 " --> pdb=" O LYS G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 456 Processing helix chain 'G' and resid 471 through 479 removed outlier: 4.084A pdb=" N MET G 475 " --> pdb=" O ASP G 471 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 493 removed outlier: 3.546A pdb=" N MET G 493 " --> pdb=" O ARG G 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.891A pdb=" N LYS H 66 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA H 67 " --> pdb=" O LYS H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 67' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.586A pdb=" N SER H 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.557A pdb=" N ASP I 86 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA I 87 " --> pdb=" O GLU I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing sheet with id=1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.885A pdb=" N GLY A 7 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 349 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS A 352 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=3, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.715A pdb=" N LEU A 308 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=5, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.555A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=7, first strand: chain 'A' and resid 111 through 113 Processing sheet with id=8, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.542A pdb=" N ALA A 245 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 174 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 223 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.647A pdb=" N THR A 236 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 197 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.988A pdb=" N VAL A 294 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=12, first strand: chain 'B' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR B 114 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 111 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 93 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 113 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 92 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR B 114 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 111 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 93 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 113 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 106 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=15, first strand: chain 'C' and resid 5 through 6 removed outlier: 4.232A pdb=" N ILE C 21 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 77 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 23 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 75 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 76 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.858A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.885A pdb=" N GLY D 7 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 349 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS D 352 " --> pdb=" O GLY D 359 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY D 359 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=19, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.714A pdb=" N LEU D 308 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=21, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.555A pdb=" N ILE D 42 " --> pdb=" O ASP D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=23, first strand: chain 'D' and resid 111 through 113 Processing sheet with id=24, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.542A pdb=" N ALA D 245 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 174 " --> pdb=" O ASP D 223 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP D 223 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'D' and resid 156 through 160 removed outlier: 3.647A pdb=" N THR D 236 " --> pdb=" O GLY D 197 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 197 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 273 through 274 removed outlier: 3.989A pdb=" N VAL D 294 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=28, first strand: chain 'E' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL E 11 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 114 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR E 93 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 113 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 92 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL E 11 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 114 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR E 93 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 113 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR E 106 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=31, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.231A pdb=" N ILE F 21 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU F 77 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR F 23 " --> pdb=" O PHE F 75 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE F 75 " --> pdb=" O TYR F 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 76 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'F' and resid 39 through 41 removed outlier: 6.858A pdb=" N TRP F 39 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.885A pdb=" N GLY G 7 " --> pdb=" O GLY G 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY G 349 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS G 352 " --> pdb=" O GLY G 359 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY G 359 " --> pdb=" O HIS G 352 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=35, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.715A pdb=" N LEU G 308 " --> pdb=" O THR G 31 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=37, first strand: chain 'G' and resid 42 through 43 removed outlier: 5.555A pdb=" N ILE G 42 " --> pdb=" O ASP G 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=37 Processing sheet with id=38, first strand: chain 'G' and resid 49 through 51 Processing sheet with id=39, first strand: chain 'G' and resid 111 through 113 Processing sheet with id=40, first strand: chain 'G' and resid 141 through 143 removed outlier: 3.542A pdb=" N ALA G 245 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE G 174 " --> pdb=" O ASP G 223 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP G 223 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 156 through 160 removed outlier: 3.647A pdb=" N THR G 236 " --> pdb=" O GLY G 197 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 197 " --> pdb=" O THR G 236 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'G' and resid 273 through 274 removed outlier: 3.988A pdb=" N VAL G 294 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=44, first strand: chain 'H' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL H 11 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR H 114 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR H 93 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 113 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE H 92 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'H' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL H 11 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR H 114 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR H 93 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 113 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR H 106 " --> pdb=" O ILE H 97 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=47, first strand: chain 'I' and resid 5 through 6 removed outlier: 4.232A pdb=" N ILE I 21 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU I 77 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR I 23 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE I 75 " --> pdb=" O TYR I 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR I 76 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.859A pdb=" N TRP I 39 " --> pdb=" O LEU I 51 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 936 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: 5.97 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4795 1.33 - 1.46: 4290 1.46 - 1.58: 7823 1.58 - 1.71: 0 1.71 - 1.84: 132 Bond restraints: 17040 Sorted by residual: bond pdb=" C HIS F 80 " pdb=" N PRO F 81 " ideal model delta sigma weight residual 1.334 1.388 -0.055 2.34e-02 1.83e+03 5.43e+00 bond pdb=" C HIS C 80 " pdb=" N PRO C 81 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.34e+00 bond pdb=" C HIS I 80 " pdb=" N PRO I 81 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.22e+00 bond pdb=" CA ARG D 100 " pdb=" C ARG D 100 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.38e-02 5.25e+03 5.19e+00 bond pdb=" C ARG G 100 " pdb=" O ARG G 100 " ideal model delta sigma weight residual 1.236 1.206 0.029 1.29e-02 6.01e+03 5.14e+00 ... (remaining 17035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 22061 2.70 - 5.39: 856 5.39 - 8.09: 95 8.09 - 10.79: 34 10.79 - 13.49: 6 Bond angle restraints: 23052 Sorted by residual: angle pdb=" N GLU A 457 " pdb=" CA GLU A 457 " pdb=" C GLU A 457 " ideal model delta sigma weight residual 109.65 100.32 9.33 1.56e+00 4.11e-01 3.58e+01 angle pdb=" N GLU D 457 " pdb=" CA GLU D 457 " pdb=" C GLU D 457 " ideal model delta sigma weight residual 109.65 100.32 9.33 1.56e+00 4.11e-01 3.58e+01 angle pdb=" N GLU G 457 " pdb=" CA GLU G 457 " pdb=" C GLU G 457 " ideal model delta sigma weight residual 109.65 100.33 9.32 1.56e+00 4.11e-01 3.57e+01 angle pdb=" C VAL G 215 " pdb=" N ASN G 216 " pdb=" CA ASN G 216 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C VAL D 215 " pdb=" N ASN D 216 " pdb=" CA ASN D 216 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 ... (remaining 23047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 9256 16.50 - 32.99: 794 32.99 - 49.49: 152 49.49 - 65.99: 33 65.99 - 82.48: 19 Dihedral angle restraints: 10254 sinusoidal: 4182 harmonic: 6072 Sorted by residual: dihedral pdb=" CA HIS I 80 " pdb=" C HIS I 80 " pdb=" N PRO I 81 " pdb=" CA PRO I 81 " ideal model delta harmonic sigma weight residual -180.00 -118.28 -61.72 0 5.00e+00 4.00e-02 1.52e+02 dihedral pdb=" CA HIS F 80 " pdb=" C HIS F 80 " pdb=" N PRO F 81 " pdb=" CA PRO F 81 " ideal model delta harmonic sigma weight residual -180.00 -118.29 -61.71 0 5.00e+00 4.00e-02 1.52e+02 dihedral pdb=" CA HIS C 80 " pdb=" C HIS C 80 " pdb=" N PRO C 81 " pdb=" CA PRO C 81 " ideal model delta harmonic sigma weight residual -180.00 -118.29 -61.71 0 5.00e+00 4.00e-02 1.52e+02 ... (remaining 10251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2148 0.093 - 0.186: 321 0.186 - 0.280: 30 0.280 - 0.373: 9 0.373 - 0.466: 3 Chirality restraints: 2511 Sorted by residual: chirality pdb=" CB ILE A 109 " pdb=" CA ILE A 109 " pdb=" CG1 ILE A 109 " pdb=" CG2 ILE A 109 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CB ILE G 109 " pdb=" CA ILE G 109 " pdb=" CG1 ILE G 109 " pdb=" CG2 ILE G 109 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CB ILE D 109 " pdb=" CA ILE D 109 " pdb=" CG1 ILE D 109 " pdb=" CG2 ILE D 109 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.41e+00 ... (remaining 2508 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 80 " 0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO C 81 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 80 " 0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO F 81 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 80 " -0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO I 81 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO I 81 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 81 " -0.046 5.00e-02 4.00e+02 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.75: 27 1.75 - 2.53: 281 2.53 - 3.32: 19491 3.32 - 4.11: 43105 4.11 - 4.90: 75703 Warning: very small nonbonded interaction distances. Nonbonded interactions: 138607 Sorted by model distance: nonbonded pdb=" CB SER A 198 " pdb=" NH2 ARG D 212 " model vdw 0.958 3.520 nonbonded pdb=" CB SER D 198 " pdb=" NH2 ARG G 212 " model vdw 0.958 3.520 nonbonded pdb=" NH2 ARG A 212 " pdb=" CB SER G 198 " model vdw 0.959 3.520 nonbonded pdb=" CB PRO A 213 " pdb=" CG2 THR G 234 " model vdw 0.990 3.860 nonbonded pdb=" CG2 THR A 234 " pdb=" CB PRO D 213 " model vdw 0.990 3.860 ... (remaining 138602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 6.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.230 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3943 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 : 0.007 0.063 17040 Z= 0.433 Angle : 1.231 13.487 23052 Z= 0.670 Chirality : 0.069 0.466 2511 Planarity : 0.008 0.083 3015 Dihedral : 13.353 82.482 6363 Min Nonbonded Distance : 0.958 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.83 % Favored : 89.03 % Rotamer: Outliers : 0.66 % Allowed : 5.70 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 8.33 % Twisted General : 1.32 % 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: -5.21 (0.13), residues: 2106 helix: -2.70 (0.25), residues: 288 sheet: -3.40 (0.19), residues: 441 loop : -3.90 (0.11), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP G 347 HIS 0.007 0.002 HIS D 9 PHE 0.033 0.005 PHE G 224 TYR 0.033 0.003 TYR D 201 ARG 0.010 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 374 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.6543 (mp) cc_final: 0.6121 (mt) REVERT: B 93 TYR cc_start: 0.7027 (m-10) cc_final: 0.6656 (m-10) REVERT: C 41 GLN cc_start: 0.5431 (tt0) cc_final: 0.4978 (tt0) REVERT: E 93 TYR cc_start: 0.4819 (m-10) cc_final: 0.4611 (m-80) REVERT: G 156 MET cc_start: 0.2299 (mpt) cc_final: 0.1726 (mtt) REVERT: G 343 LEU cc_start: 0.3177 (mm) cc_final: 0.2900 (mt) outliers start: 12 outliers final: 0 residues processed: 383 average time/residue: 1.1941 time to fit residues: 516.1930 Evaluate side-chains 183 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN A 176 HIS A 388 GLN A 421 ASN A 430 ASN A 431 GLN A 481 ASN A 485 HIS ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN D 202 GLN D 405 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 485 HIS E 56 ASN F 78 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 405 ASN G 430 ASN ** G 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN G 485 HIS ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN I 78 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17040 Z= 0.339 Angle : 0.910 12.882 23052 Z= 0.476 Chirality : 0.054 0.284 2511 Planarity : 0.013 0.356 3015 Dihedral : 9.461 67.125 2502 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.07 % Favored : 89.89 % Rotamer: Outliers : 4.43 % Allowed : 13.84 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.29 % 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: -4.60 (0.14), residues: 2106 helix: -2.21 (0.24), residues: 288 sheet: -2.77 (0.21), residues: 459 loop : -3.57 (0.12), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP G 409 HIS 0.008 0.002 HIS D 485 PHE 0.028 0.003 PHE G 224 TYR 0.024 0.003 TYR D 201 ARG 0.057 0.002 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 281 time to evaluate : 1.936 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 475 MET cc_start: 0.4167 (mmt) cc_final: 0.3759 (mpp) REVERT: B 37 LYS cc_start: 0.8125 (tttt) cc_final: 0.7885 (tmmt) REVERT: B 42 LYS cc_start: 0.5872 (mttm) cc_final: 0.5669 (mmtp) REVERT: B 69 MET cc_start: 0.1691 (OUTLIER) cc_final: 0.0836 (tpt) REVERT: B 80 MET cc_start: 0.4263 (tpt) cc_final: 0.4037 (tpt) REVERT: C 49 ARG cc_start: 0.6674 (ptp-170) cc_final: 0.6372 (pmt170) REVERT: D 449 LYS cc_start: 0.3886 (mmpt) cc_final: 0.2820 (tptt) REVERT: E 80 MET cc_start: 0.2463 (tpt) cc_final: 0.2223 (tmm) REVERT: G 156 MET cc_start: 0.3548 (mpt) cc_final: 0.3063 (mtt) REVERT: G 257 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.4275 (pmm) REVERT: G 475 MET cc_start: 0.3324 (mpt) cc_final: 0.2918 (mpt) REVERT: H 49 VAL cc_start: 0.3360 (p) cc_final: 0.2708 (t) outliers start: 80 outliers final: 23 residues processed: 334 average time/residue: 1.1590 time to fit residues: 437.1290 Evaluate side-chains 216 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 480 ASN Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS A 225 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 432 HIS A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 176 HIS D 405 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN G 175 HIS G 176 HIS ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 GLN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.8688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.129 17040 Z= 0.600 Angle : 1.135 18.845 23052 Z= 0.593 Chirality : 0.063 0.318 2511 Planarity : 0.011 0.295 3015 Dihedral : 10.944 169.064 2502 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 29.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.10 % Favored : 85.80 % Rotamer: Outliers : 6.70 % Allowed : 18.22 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.88 % 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: -4.65 (0.15), residues: 2106 helix: -2.06 (0.26), residues: 279 sheet: -2.99 (0.23), residues: 396 loop : -3.58 (0.13), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 340 HIS 0.018 0.003 HIS G 275 PHE 0.051 0.005 PHE A 464 TYR 0.046 0.004 TYR D 348 ARG 0.037 0.002 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 238 time to evaluate : 1.831 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 82 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6429 (mtp85) REVERT: A 104 ARG cc_start: 0.6396 (ptt180) cc_final: 0.5829 (ptp90) REVERT: A 193 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6432 (tt) REVERT: A 335 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.5395 (p90) REVERT: A 449 LYS cc_start: 0.4906 (mptt) cc_final: 0.4682 (mptt) REVERT: A 467 PHE cc_start: 0.4549 (OUTLIER) cc_final: 0.4257 (m-10) REVERT: A 493 MET cc_start: -0.0654 (mtt) cc_final: -0.2829 (ttm) REVERT: B 69 MET cc_start: 0.2854 (tpt) cc_final: 0.1900 (tpt) REVERT: D 114 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6924 (mtm) REVERT: D 493 MET cc_start: -0.0739 (mtt) cc_final: -0.0998 (mtt) REVERT: E 80 MET cc_start: 0.4115 (tpt) cc_final: 0.3698 (tmm) REVERT: G 4 ILE cc_start: 0.8134 (pt) cc_final: 0.7882 (pp) REVERT: G 388 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6911 (tp40) REVERT: G 418 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6708 (m-10) REVERT: G 447 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4894 (ppt170) REVERT: G 464 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7149 (t80) REVERT: G 465 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5446 (tm-30) REVERT: H 33 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.5217 (tmm) outliers start: 121 outliers final: 40 residues processed: 326 average time/residue: 1.0881 time to fit residues: 402.5403 Evaluate side-chains 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 388 GLN Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 GLN G 388 GLN G 430 ASN G 431 GLN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.8856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17040 Z= 0.273 Angle : 0.849 14.605 23052 Z= 0.436 Chirality : 0.051 0.262 2511 Planarity : 0.007 0.216 3015 Dihedral : 10.433 176.852 2502 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.02 % Favored : 90.93 % Rotamer: Outliers : 5.43 % Allowed : 20.87 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.54 % 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: -4.40 (0.15), residues: 2106 helix: -1.70 (0.26), residues: 282 sheet: -2.96 (0.21), residues: 474 loop : -3.37 (0.13), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 409 HIS 0.009 0.002 HIS F 80 PHE 0.037 0.003 PHE A 464 TYR 0.022 0.002 TYR H 26 ARG 0.020 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 225 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LYS cc_start: 0.4759 (mptt) cc_final: 0.4450 (mptt) REVERT: A 475 MET cc_start: 0.4252 (mmt) cc_final: 0.3862 (mpp) REVERT: A 493 MET cc_start: -0.1075 (mtt) cc_final: -0.3053 (ttm) REVERT: B 69 MET cc_start: 0.1990 (OUTLIER) cc_final: 0.1221 (tpt) REVERT: C 79 ILE cc_start: 0.3339 (OUTLIER) cc_final: 0.2870 (mp) REVERT: D 57 LEU cc_start: 0.6819 (tp) cc_final: 0.6468 (tp) REVERT: D 114 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6817 (mtm) REVERT: D 358 GLU cc_start: 0.7475 (tp30) cc_final: 0.7141 (tp30) REVERT: D 436 LEU cc_start: 0.5964 (pt) cc_final: 0.5752 (pt) REVERT: D 493 MET cc_start: -0.0527 (mtt) cc_final: -0.0778 (mtt) REVERT: E 47 ILE cc_start: 0.3909 (OUTLIER) cc_final: 0.3651 (pp) REVERT: E 80 MET cc_start: 0.4027 (tpt) cc_final: 0.3756 (tmm) REVERT: G 92 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6103 (pttm) REVERT: G 465 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.4978 (tm-30) REVERT: H 33 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.5295 (tmm) outliers start: 98 outliers final: 39 residues processed: 296 average time/residue: 1.1421 time to fit residues: 387.0246 Evaluate side-chains 218 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 0.0050 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 50 optimal weight: 0.0170 overall best weight: 1.1236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN F 57 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.9191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17040 Z= 0.309 Angle : 0.844 13.139 23052 Z= 0.436 Chirality : 0.052 0.402 2511 Planarity : 0.007 0.151 3015 Dihedral : 9.521 109.885 2502 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.97 % Favored : 87.99 % Rotamer: Outliers : 5.92 % Allowed : 22.26 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.44 % 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: -4.30 (0.15), residues: 2106 helix: -1.53 (0.26), residues: 282 sheet: -2.95 (0.21), residues: 480 loop : -3.30 (0.13), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 409 HIS 0.008 0.002 HIS F 80 PHE 0.039 0.003 PHE A 93 TYR 0.020 0.002 TYR H 26 ARG 0.025 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 194 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6522 (mtp85) REVERT: A 193 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6383 (tt) REVERT: A 449 LYS cc_start: 0.4658 (mptt) cc_final: 0.4435 (mptt) REVERT: A 475 MET cc_start: 0.4269 (mmt) cc_final: 0.3875 (mpp) REVERT: A 493 MET cc_start: -0.0755 (mtt) cc_final: -0.2871 (ttm) REVERT: B 69 MET cc_start: 0.2077 (tpt) cc_final: 0.1343 (tpt) REVERT: C 79 ILE cc_start: 0.3273 (OUTLIER) cc_final: 0.2797 (mp) REVERT: D 4 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6645 (pt) REVERT: D 493 MET cc_start: -0.0367 (mtt) cc_final: -0.0626 (mtt) REVERT: E 80 MET cc_start: 0.4400 (tpt) cc_final: 0.4090 (tmm) REVERT: G 92 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6366 (pttm) REVERT: H 33 MET cc_start: 0.5827 (OUTLIER) cc_final: 0.5466 (tmm) outliers start: 107 outliers final: 55 residues processed: 274 average time/residue: 1.0373 time to fit residues: 325.1022 Evaluate side-chains 232 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.9463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17040 Z= 0.275 Angle : 0.829 12.670 23052 Z= 0.424 Chirality : 0.051 0.419 2511 Planarity : 0.006 0.165 3015 Dihedral : 9.677 111.597 2502 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.78 % Favored : 90.17 % Rotamer: Outliers : 6.04 % Allowed : 22.43 % Favored : 71.54 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.44 % 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: -4.13 (0.15), residues: 2106 helix: -1.37 (0.27), residues: 282 sheet: -2.81 (0.21), residues: 480 loop : -3.21 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 409 HIS 0.006 0.002 HIS B 34 PHE 0.033 0.003 PHE D 464 TYR 0.021 0.002 TYR H 26 ARG 0.024 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 191 time to evaluate : 2.178 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 447 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.3095 (ptt90) REVERT: A 449 LYS cc_start: 0.4881 (mptt) cc_final: 0.4642 (mptt) REVERT: A 467 PHE cc_start: 0.4543 (OUTLIER) cc_final: 0.4247 (m-10) REVERT: A 493 MET cc_start: -0.1170 (mtt) cc_final: -0.3103 (ttm) REVERT: B 37 LYS cc_start: 0.7959 (tmmt) cc_final: 0.7737 (tmmt) REVERT: B 46 TRP cc_start: 0.1839 (t60) cc_final: 0.1532 (t60) REVERT: B 69 MET cc_start: 0.1926 (OUTLIER) cc_final: 0.1058 (tpt) REVERT: C 79 ILE cc_start: 0.3211 (OUTLIER) cc_final: 0.2779 (mp) REVERT: D 9 HIS cc_start: 0.6809 (OUTLIER) cc_final: 0.5477 (p-80) REVERT: D 114 MET cc_start: 0.7342 (mmm) cc_final: 0.6799 (mtm) REVERT: D 436 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.5917 (pp) REVERT: E 80 MET cc_start: 0.4822 (tpt) cc_final: 0.4544 (tmm) REVERT: F 79 ILE cc_start: 0.2958 (OUTLIER) cc_final: 0.2091 (tt) REVERT: G 9 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.5743 (p-80) REVERT: G 92 LYS cc_start: 0.6617 (OUTLIER) cc_final: 0.6161 (pttm) REVERT: H 33 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5620 (tmm) REVERT: H 69 MET cc_start: 0.0553 (pmt) cc_final: -0.0293 (pmt) REVERT: I 79 ILE cc_start: 0.5302 (OUTLIER) cc_final: 0.4786 (mt) outliers start: 109 outliers final: 61 residues processed: 278 average time/residue: 1.0573 time to fit residues: 335.2219 Evaluate side-chains 242 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 432 HIS Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 388 GLN B 38 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.9687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17040 Z= 0.260 Angle : 0.818 13.288 23052 Z= 0.416 Chirality : 0.051 0.411 2511 Planarity : 0.007 0.136 3015 Dihedral : 9.308 111.489 2502 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 5.87 % Allowed : 23.20 % Favored : 70.93 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 5.56 % Twisted General : 0.24 % 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: -4.01 (0.15), residues: 2106 helix: -1.31 (0.27), residues: 291 sheet: -2.83 (0.21), residues: 486 loop : -3.07 (0.14), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 340 HIS 0.006 0.001 HIS I 80 PHE 0.027 0.003 PHE A 464 TYR 0.017 0.002 TYR C 91 ARG 0.076 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 190 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LEU cc_start: 0.4496 (OUTLIER) cc_final: 0.3982 (tp) REVERT: A 447 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.3203 (ptt90) REVERT: A 449 LYS cc_start: 0.4736 (OUTLIER) cc_final: 0.4487 (mptt) REVERT: A 465 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5551 (pp20) REVERT: A 467 PHE cc_start: 0.4573 (OUTLIER) cc_final: 0.4306 (m-80) REVERT: A 493 MET cc_start: -0.1214 (mtt) cc_final: -0.3126 (ttm) REVERT: B 37 LYS cc_start: 0.8017 (tmmt) cc_final: 0.7756 (tmmt) REVERT: B 46 TRP cc_start: 0.1856 (t60) cc_final: 0.1527 (t60) REVERT: B 69 MET cc_start: 0.1767 (OUTLIER) cc_final: 0.0905 (tpt) REVERT: C 79 ILE cc_start: 0.3180 (OUTLIER) cc_final: 0.2761 (mp) REVERT: D 9 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.5277 (p-80) REVERT: D 101 GLN cc_start: 0.4705 (OUTLIER) cc_final: 0.4490 (mt0) REVERT: D 114 MET cc_start: 0.7306 (mmm) cc_final: 0.6766 (mtm) REVERT: D 212 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.4776 (tmt170) REVERT: D 436 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.5916 (pp) REVERT: E 42 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6923 (pmtt) REVERT: E 80 MET cc_start: 0.4966 (tpt) cc_final: 0.4691 (tmm) REVERT: F 49 ARG cc_start: 0.6997 (ptp-170) cc_final: 0.6713 (pmt170) REVERT: F 79 ILE cc_start: 0.2687 (OUTLIER) cc_final: 0.1788 (tt) REVERT: G 92 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6121 (pttm) REVERT: H 19 ILE cc_start: 0.2757 (tp) cc_final: 0.2530 (tp) REVERT: H 33 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.5661 (tmm) REVERT: H 69 MET cc_start: 0.0485 (OUTLIER) cc_final: -0.0434 (pmt) REVERT: I 79 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4395 (mt) outliers start: 106 outliers final: 62 residues processed: 273 average time/residue: 1.0753 time to fit residues: 334.9399 Evaluate side-chains 249 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 171 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.9860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17040 Z= 0.268 Angle : 0.833 14.150 23052 Z= 0.423 Chirality : 0.051 0.415 2511 Planarity : 0.006 0.130 3015 Dihedral : 9.588 111.574 2502 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 5.43 % Allowed : 23.98 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.20 % 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: -3.91 (0.16), residues: 2106 helix: -1.32 (0.26), residues: 291 sheet: -2.68 (0.22), residues: 480 loop : -3.02 (0.14), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 409 HIS 0.006 0.001 HIS I 80 PHE 0.037 0.003 PHE A 93 TYR 0.018 0.002 TYR G 445 ARG 0.043 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 184 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4178 (tp) REVERT: A 444 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6455 (tt) REVERT: A 447 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.3252 (ptt90) REVERT: A 449 LYS cc_start: 0.4730 (OUTLIER) cc_final: 0.4476 (mptt) REVERT: A 465 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5342 (pp20) REVERT: A 467 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.4407 (m-80) REVERT: A 493 MET cc_start: -0.1433 (mtt) cc_final: -0.3265 (ttm) REVERT: B 37 LYS cc_start: 0.8001 (tmmt) cc_final: 0.7740 (tmmt) REVERT: B 46 TRP cc_start: 0.1708 (t60) cc_final: 0.1396 (t60) REVERT: B 69 MET cc_start: 0.1615 (OUTLIER) cc_final: 0.0757 (tpt) REVERT: C 79 ILE cc_start: 0.3209 (OUTLIER) cc_final: 0.2819 (mp) REVERT: D 9 HIS cc_start: 0.6578 (OUTLIER) cc_final: 0.5781 (p-80) REVERT: D 114 MET cc_start: 0.7348 (mmm) cc_final: 0.6774 (mtm) REVERT: D 212 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.5281 (tmt170) REVERT: D 436 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5952 (pp) REVERT: E 80 MET cc_start: 0.4986 (tpt) cc_final: 0.4690 (tmm) REVERT: G 92 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6255 (pttm) REVERT: G 255 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6099 (ttpp) REVERT: G 449 LYS cc_start: 0.4730 (mptt) cc_final: 0.4518 (mptt) REVERT: H 33 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5790 (tmm) REVERT: H 69 MET cc_start: 0.0471 (OUTLIER) cc_final: -0.0519 (pmt) REVERT: H 82 LEU cc_start: 0.5376 (mp) cc_final: 0.4636 (mt) REVERT: I 13 VAL cc_start: 0.6145 (OUTLIER) cc_final: 0.5627 (t) REVERT: I 17 GLN cc_start: 0.4296 (tt0) cc_final: 0.4058 (tt0) REVERT: I 79 ILE cc_start: 0.4657 (OUTLIER) cc_final: 0.3914 (mt) outliers start: 98 outliers final: 59 residues processed: 262 average time/residue: 1.0792 time to fit residues: 322.3164 Evaluate side-chains 243 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 1.0060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17040 Z= 0.248 Angle : 0.816 15.198 23052 Z= 0.413 Chirality : 0.051 0.422 2511 Planarity : 0.007 0.142 3015 Dihedral : 9.532 109.816 2502 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.71 % Allowed : 25.53 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.15 % 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: -3.76 (0.16), residues: 2106 helix: -1.10 (0.27), residues: 291 sheet: -2.60 (0.22), residues: 486 loop : -2.93 (0.14), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 409 HIS 0.006 0.001 HIS I 80 PHE 0.030 0.002 PHE A 93 TYR 0.018 0.002 TYR G 445 ARG 0.047 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 189 time to evaluate : 1.999 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 308 LEU cc_start: 0.5934 (pt) cc_final: 0.5588 (tp) REVERT: A 343 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4258 (tp) REVERT: A 444 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6213 (tt) REVERT: A 447 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.3013 (ptt90) REVERT: A 449 LYS cc_start: 0.4465 (OUTLIER) cc_final: 0.4110 (mptt) REVERT: A 465 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.5405 (pp20) REVERT: A 467 PHE cc_start: 0.4877 (OUTLIER) cc_final: 0.4607 (m-80) REVERT: B 37 LYS cc_start: 0.7955 (tmmt) cc_final: 0.6541 (ptmm) REVERT: B 46 TRP cc_start: 0.1488 (t60) cc_final: 0.1268 (t60) REVERT: B 49 VAL cc_start: 0.4937 (OUTLIER) cc_final: 0.4614 (p) REVERT: B 69 MET cc_start: 0.1491 (OUTLIER) cc_final: 0.0646 (tpt) REVERT: C 79 ILE cc_start: 0.2994 (OUTLIER) cc_final: 0.2648 (mp) REVERT: D 9 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.5971 (p-80) REVERT: D 47 LYS cc_start: 0.6842 (ptpp) cc_final: 0.6620 (ptmm) REVERT: D 114 MET cc_start: 0.7319 (mmm) cc_final: 0.6762 (mtm) REVERT: D 212 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.4496 (tmt170) REVERT: D 436 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5915 (pp) REVERT: D 452 LEU cc_start: 0.3671 (OUTLIER) cc_final: 0.3400 (tm) REVERT: E 42 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6923 (pmtt) REVERT: E 80 MET cc_start: 0.5120 (tpt) cc_final: 0.4825 (tmm) REVERT: F 79 ILE cc_start: 0.3026 (OUTLIER) cc_final: 0.2305 (mp) REVERT: G 92 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6320 (pttm) REVERT: G 255 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5947 (ttpp) REVERT: H 19 ILE cc_start: 0.2997 (tp) cc_final: 0.2795 (tp) REVERT: I 13 VAL cc_start: 0.6594 (OUTLIER) cc_final: 0.6259 (t) REVERT: I 79 ILE cc_start: 0.4628 (OUTLIER) cc_final: 0.4241 (mp) outliers start: 85 outliers final: 56 residues processed: 253 average time/residue: 1.0443 time to fit residues: 301.3341 Evaluate side-chains 245 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 171 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.0970 chunk 119 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 388 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 1.0237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17040 Z= 0.289 Angle : 0.870 15.719 23052 Z= 0.442 Chirality : 0.052 0.398 2511 Planarity : 0.006 0.124 3015 Dihedral : 9.737 111.118 2502 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 5.09 % Allowed : 26.02 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 5.56 % Twisted General : 0.15 % 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: -3.76 (0.16), residues: 2106 helix: -1.10 (0.27), residues: 291 sheet: -2.51 (0.23), residues: 474 loop : -2.97 (0.14), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 409 HIS 0.007 0.001 HIS I 80 PHE 0.033 0.003 PHE D 464 TYR 0.016 0.002 TYR D 89 ARG 0.030 0.001 ARG A 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 183 time to evaluate : 1.788 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 82 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6630 (mtp85) REVERT: A 343 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4234 (tp) REVERT: A 444 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6461 (tt) REVERT: A 447 ARG cc_start: 0.5627 (OUTLIER) cc_final: 0.3219 (ptt90) REVERT: A 465 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5358 (pp20) REVERT: A 467 PHE cc_start: 0.5341 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: B 46 TRP cc_start: 0.1595 (t60) cc_final: 0.1220 (t60) REVERT: B 49 VAL cc_start: 0.4768 (OUTLIER) cc_final: 0.4424 (p) REVERT: B 69 MET cc_start: 0.1742 (OUTLIER) cc_final: 0.0858 (tpt) REVERT: B 93 TYR cc_start: 0.7385 (m-10) cc_final: 0.7147 (m-10) REVERT: C 79 ILE cc_start: 0.3118 (OUTLIER) cc_final: 0.2722 (mp) REVERT: C 100 ARG cc_start: 0.1356 (mtt90) cc_final: 0.1102 (tmm160) REVERT: D 9 HIS cc_start: 0.6449 (OUTLIER) cc_final: 0.6036 (p-80) REVERT: D 45 LYS cc_start: 0.6687 (tmmt) cc_final: 0.6484 (ttmt) REVERT: D 47 LYS cc_start: 0.6834 (ptpp) cc_final: 0.6374 (ptmm) REVERT: D 114 MET cc_start: 0.7338 (mmm) cc_final: 0.6755 (mtm) REVERT: D 212 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.4371 (tmt170) REVERT: D 436 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6005 (pp) REVERT: E 42 LYS cc_start: 0.7350 (mmmt) cc_final: 0.6367 (mmtp) REVERT: E 80 MET cc_start: 0.5196 (tpt) cc_final: 0.4878 (tmm) REVERT: F 79 ILE cc_start: 0.2976 (OUTLIER) cc_final: 0.2284 (mp) REVERT: G 92 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6431 (pttm) REVERT: G 255 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.6028 (ttpp) REVERT: I 13 VAL cc_start: 0.6130 (OUTLIER) cc_final: 0.5847 (t) REVERT: I 49 ARG cc_start: 0.6410 (ptt180) cc_final: 0.6027 (ppt170) REVERT: I 79 ILE cc_start: 0.4570 (OUTLIER) cc_final: 0.4182 (mp) outliers start: 92 outliers final: 56 residues processed: 253 average time/residue: 1.1204 time to fit residues: 323.0800 Evaluate side-chains 244 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 171 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 164 optimal weight: 0.0020 chunk 68 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 387 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.175345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.134196 restraints weight = 24953.641| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 2.90 r_work: 0.4447 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 1.0359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17040 Z= 0.261 Angle : 0.853 17.152 23052 Z= 0.432 Chirality : 0.051 0.391 2511 Planarity : 0.007 0.128 3015 Dihedral : 9.639 109.882 2502 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.49 % Allowed : 26.91 % Favored : 68.60 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: -3.64 (0.16), residues: 2106 helix: -0.99 (0.28), residues: 291 sheet: -2.37 (0.23), residues: 474 loop : -2.92 (0.14), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 409 HIS 0.007 0.001 HIS I 80 PHE 0.029 0.002 PHE A 93 TYR 0.016 0.002 TYR G 201 ARG 0.025 0.001 ARG A 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6421.00 seconds wall clock time: 116 minutes 52.88 seconds (7012.88 seconds total)