Starting phenix.real_space_refine on Mon Nov 18 14:37:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv0_35735/11_2024/8iv0_35735.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv0_35735/11_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv0_35735/11_2024/8iv0_35735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv0_35735/11_2024/8iv0_35735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv0_35735/11_2024/8iv0_35735.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv0_35735/11_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.26, 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=0, 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 " Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 2.2 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: 2.21 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: 5.51 Time building geometry restraints manager: 4.67 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: 0.44 - 1.34: 27 1.34 - 2.23: 98 2.23 - 3.12: 12181 3.12 - 4.01: 45165 4.01 - 4.90: 81166 Warning: very small nonbonded interaction distances. Nonbonded interactions: 138637 Sorted by model distance: nonbonded pdb=" NE ARG A 212 " pdb=" CA SER G 198 " model vdw 0.445 3.550 nonbonded pdb=" CA SER A 198 " pdb=" NE ARG D 212 " model vdw 0.445 3.550 nonbonded pdb=" CA SER D 198 " pdb=" NE ARG G 212 " model vdw 0.446 3.550 nonbonded pdb=" CG1 ILE A 102 " pdb=" NZ LYS D 401 " model vdw 0.833 3.520 nonbonded pdb=" NZ LYS A 401 " pdb=" CG1 ILE G 102 " model vdw 0.833 3.520 ... (remaining 138632 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 38.110 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.220 ------------------------------------------------------------------------------- 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= 0.425 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 : 0.445 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 : 1.747 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: 1.1642 time to fit residues: 503.4598 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 : 1.903 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 485 HIS E 56 ASN F 78 ASN ** F 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17040 Z= 0.313 Angle : 0.912 12.947 23052 Z= 0.477 Chirality : 0.053 0.216 2511 Planarity : 0.008 0.093 3015 Dihedral : 9.385 59.240 2502 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.02 % Favored : 89.93 % Rotamer: Outliers : 4.54 % Allowed : 14.06 % Favored : 81.40 % 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: -4.58 (0.14), residues: 2106 helix: -1.99 (0.26), residues: 270 sheet: -2.76 (0.21), residues: 459 loop : -3.59 (0.12), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G 409 HIS 0.008 0.002 HIS D 485 PHE 0.029 0.003 PHE G 224 TYR 0.025 0.003 TYR A 348 ARG 0.012 0.001 ARG D 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: 82 poor density : 279 time to evaluate : 1.771 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 475 MET cc_start: 0.4170 (mmt) cc_final: 0.3759 (mpp) REVERT: B 42 LYS cc_start: 0.5877 (mttm) cc_final: 0.5677 (mmtp) REVERT: B 63 PHE cc_start: 0.3331 (m-80) cc_final: 0.3116 (m-80) REVERT: B 69 MET cc_start: 0.1749 (OUTLIER) cc_final: 0.0911 (tpt) REVERT: B 80 MET cc_start: 0.4295 (tpt) cc_final: 0.4088 (tpt) REVERT: B 84 ARG cc_start: 0.3123 (pmt-80) cc_final: 0.2454 (pmt170) REVERT: D 449 LYS cc_start: 0.3888 (mmpt) cc_final: 0.2831 (tptt) REVERT: E 80 MET cc_start: 0.2464 (tpt) cc_final: 0.2208 (tmm) REVERT: G 156 MET cc_start: 0.3928 (mpt) cc_final: 0.3489 (mtt) REVERT: G 257 MET cc_start: 0.5809 (OUTLIER) cc_final: 0.4242 (pmm) REVERT: G 475 MET cc_start: 0.3301 (mpt) cc_final: 0.2885 (mpt) REVERT: H 49 VAL cc_start: 0.3327 (p) cc_final: 0.2666 (t) outliers start: 82 outliers final: 22 residues processed: 334 average time/residue: 1.1348 time to fit residues: 427.8971 Evaluate side-chains 207 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 175 HIS A 225 HIS 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 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN D 430 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.8137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17040 Z= 0.387 Angle : 0.929 12.580 23052 Z= 0.483 Chirality : 0.055 0.259 2511 Planarity : 0.007 0.113 3015 Dihedral : 9.819 90.035 2502 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 6.20 % Allowed : 17.72 % Favored : 76.08 % 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: -4.53 (0.15), residues: 2106 helix: -2.15 (0.25), residues: 300 sheet: -2.95 (0.22), residues: 423 loop : -3.44 (0.13), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 340 HIS 0.011 0.002 HIS D 275 PHE 0.040 0.004 PHE A 464 TYR 0.030 0.003 TYR D 348 ARG 0.034 0.001 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 361 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 249 time to evaluate : 1.881 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: 0.6837 (OUTLIER) cc_final: 0.6541 (mtp85) REVERT: A 193 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6319 (tt) REVERT: A 335 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5262 (p90) REVERT: A 447 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.2759 (ptt90) REVERT: A 467 PHE cc_start: 0.4401 (OUTLIER) cc_final: 0.4167 (m-10) REVERT: A 493 MET cc_start: -0.0672 (mtt) cc_final: -0.2768 (ttm) REVERT: B 37 LYS cc_start: 0.8100 (tmmt) cc_final: 0.7825 (tmmt) REVERT: B 63 PHE cc_start: 0.3488 (m-80) cc_final: 0.3247 (m-80) REVERT: B 69 MET cc_start: 0.2293 (tpt) cc_final: 0.1841 (tpt) REVERT: C 49 ARG cc_start: 0.6958 (ptp-170) cc_final: 0.6653 (pmt170) REVERT: D 101 GLN cc_start: 0.5347 (OUTLIER) cc_final: 0.5107 (mt0) REVERT: D 104 ARG cc_start: 0.6067 (ptt180) cc_final: 0.5768 (ptp-170) REVERT: D 114 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6746 (mtm) REVERT: D 425 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6641 (pp) REVERT: D 493 MET cc_start: -0.0872 (mtt) cc_final: -0.1201 (mtt) REVERT: E 80 MET cc_start: 0.3737 (tpt) cc_final: 0.3336 (tmm) REVERT: G 388 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: G 465 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5001 (tm-30) REVERT: H 33 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.4874 (tmm) REVERT: H 69 MET cc_start: -0.0577 (OUTLIER) cc_final: -0.1707 (pmm) outliers start: 112 outliers final: 31 residues processed: 332 average time/residue: 1.0540 time to fit residues: 399.4263 Evaluate side-chains 239 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 82 ARG Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR 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 385 THR 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 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 92 CYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 101 GLN 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 425 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 388 GLN 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 69 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 481 ASN ** 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 176 HIS E 60 ASN F 57 ASN ** 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 432 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17040 Z= 0.239 Angle : 0.771 12.305 23052 Z= 0.396 Chirality : 0.049 0.241 2511 Planarity : 0.006 0.071 3015 Dihedral : 9.298 101.655 2502 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.09 % Allowed : 20.87 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.34 % 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: -4.24 (0.15), residues: 2106 helix: -1.63 (0.26), residues: 288 sheet: -3.02 (0.20), residues: 510 loop : -3.16 (0.14), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 409 HIS 0.007 0.001 HIS F 80 PHE 0.033 0.003 PHE G 464 TYR 0.017 0.002 TYR F 23 ARG 0.009 0.001 ARG A 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 321 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 229 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.2795 (ptt90) REVERT: A 475 MET cc_start: 0.4170 (mmt) cc_final: 0.3924 (mpp) REVERT: A 493 MET cc_start: -0.0660 (mtt) cc_final: -0.2795 (ttm) REVERT: B 37 LYS cc_start: 0.8088 (tmmt) cc_final: 0.7694 (tmmt) REVERT: B 46 TRP cc_start: 0.1791 (t60) cc_final: 0.1570 (t60) REVERT: B 69 MET cc_start: 0.1503 (tpt) cc_final: 0.0986 (tpt) REVERT: C 49 ARG cc_start: 0.6676 (ptp-170) cc_final: 0.6466 (ptp-170) REVERT: C 79 ILE cc_start: 0.3327 (OUTLIER) cc_final: 0.2831 (mp) REVERT: D 104 ARG cc_start: 0.5873 (ptt180) cc_final: 0.5448 (ptp-170) REVERT: D 114 MET cc_start: 0.7259 (mmm) cc_final: 0.6692 (mtm) REVERT: D 493 MET cc_start: -0.0524 (mtt) cc_final: -0.0775 (mtt) REVERT: E 42 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7179 (pptt) REVERT: E 80 MET cc_start: 0.3782 (tpt) cc_final: 0.3472 (tmm) REVERT: F 4 MET cc_start: 0.2624 (mmt) cc_final: 0.2356 (mmp) REVERT: H 33 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5030 (tmt) REVERT: I 78 ASN cc_start: 0.4150 (p0) cc_final: 0.3518 (t0) outliers start: 92 outliers final: 36 residues processed: 298 average time/residue: 1.0160 time to fit residues: 348.4531 Evaluate side-chains 223 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR 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 447 ARG 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 106 TYR Chi-restraints excluded: chain C residue 50 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 27 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 94 VAL 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 263 VAL Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 385 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 I residue 10 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 314 ASN A 432 HIS A 481 ASN ** 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** 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 225 HIS ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.9358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17040 Z= 0.423 Angle : 0.929 13.624 23052 Z= 0.481 Chirality : 0.056 0.259 2511 Planarity : 0.007 0.084 3015 Dihedral : 9.874 110.484 2502 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 5.87 % Allowed : 21.87 % Favored : 72.26 % 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: -4.31 (0.15), residues: 2106 helix: -1.75 (0.25), residues: 297 sheet: -2.99 (0.22), residues: 435 loop : -3.27 (0.13), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP G 409 HIS 0.013 0.003 HIS D 8 PHE 0.048 0.004 PHE A 464 TYR 0.038 0.003 TYR D 201 ARG 0.013 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 313 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 207 time to evaluate : 1.844 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: 0.6767 (OUTLIER) cc_final: 0.6502 (mtp85) REVERT: A 193 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6433 (tt) REVERT: A 444 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6518 (tt) REVERT: A 447 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.3159 (ptt90) REVERT: A 449 LYS cc_start: 0.4792 (mptt) cc_final: 0.4585 (mptt) REVERT: A 475 MET cc_start: 0.4406 (mmt) cc_final: 0.3736 (mpp) REVERT: A 493 MET cc_start: -0.1154 (mtt) cc_final: -0.3060 (ttm) REVERT: B 37 LYS cc_start: 0.8132 (tmmt) cc_final: 0.7725 (tmmt) REVERT: B 69 MET cc_start: 0.2385 (tpt) cc_final: 0.1589 (tpt) REVERT: C 49 ARG cc_start: 0.7003 (ptp-170) cc_final: 0.6745 (ptp-170) REVERT: C 79 ILE cc_start: 0.3225 (OUTLIER) cc_final: 0.2770 (mp) REVERT: D 9 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6035 (p-80) REVERT: E 80 MET cc_start: 0.4552 (tpt) cc_final: 0.4200 (tmm) REVERT: F 4 MET cc_start: 0.2890 (mmt) cc_final: 0.2119 (mmp) REVERT: G 36 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5955 (ptt180) REVERT: H 33 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5486 (tmm) outliers start: 106 outliers final: 50 residues processed: 287 average time/residue: 0.9921 time to fit residues: 327.7065 Evaluate side-chains 228 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 37 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 112 GLU 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 308 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 465 GLU Chi-restraints excluded: chain A residue 471 ASP 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 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 49 THR Chi-restraints excluded: chain D residue 123 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 263 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 110 ASP 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 178 VAL Chi-restraints excluded: chain G residue 180 THR 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 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 I residue 21 ILE Chi-restraints excluded: chain I residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 5.9990 chunk 180 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.0270 chunk 105 optimal weight: 0.9980 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 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** ** 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 388 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.9545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17040 Z= 0.263 Angle : 0.818 12.905 23052 Z= 0.419 Chirality : 0.051 0.377 2511 Planarity : 0.006 0.068 3015 Dihedral : 9.632 111.380 2502 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.20 % Allowed : 22.65 % Favored : 72.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 5.56 % Twisted General : 0.34 % 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: -4.10 (0.15), residues: 2106 helix: -1.62 (0.26), residues: 300 sheet: -2.84 (0.21), residues: 492 loop : -3.09 (0.14), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 46 HIS 0.008 0.001 HIS F 80 PHE 0.039 0.003 PHE A 93 TYR 0.019 0.002 TYR D 201 ARG 0.011 0.001 ARG C 100 *********************** 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 295 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 201 time to evaluate : 1.924 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 381 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6315 (tm) REVERT: A 444 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6466 (tt) REVERT: A 447 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.3055 (ptt90) REVERT: A 467 PHE cc_start: 0.4513 (OUTLIER) cc_final: 0.4242 (OUTLIER) REVERT: A 493 MET cc_start: -0.1175 (mtt) cc_final: -0.3132 (ttm) REVERT: B 37 LYS cc_start: 0.8032 (tmmt) cc_final: 0.7644 (tmmt) REVERT: B 69 MET cc_start: 0.1848 (tpt) cc_final: 0.1175 (tpt) REVERT: C 79 ILE cc_start: 0.3344 (OUTLIER) cc_final: 0.2918 (mp) REVERT: D 114 MET cc_start: 0.7399 (mmm) cc_final: 0.6780 (mtm) REVERT: E 42 LYS cc_start: 0.7481 (mmmt) cc_final: 0.6971 (pptt) REVERT: E 80 MET cc_start: 0.4856 (tpt) cc_final: 0.4573 (tmm) REVERT: F 4 MET cc_start: 0.2764 (mmt) cc_final: 0.2247 (mmp) REVERT: F 65 ARG cc_start: 0.2600 (OUTLIER) cc_final: 0.1948 (ppt170) REVERT: F 79 ILE cc_start: 0.2853 (OUTLIER) cc_final: 0.2099 (tt) REVERT: G 193 LEU cc_start: 0.6881 (mm) cc_final: 0.6566 (mp) REVERT: G 441 MET cc_start: 0.4721 (mmt) cc_final: 0.4366 (mmt) outliers start: 94 outliers final: 47 residues processed: 273 average time/residue: 1.0260 time to fit residues: 321.6735 Evaluate side-chains 228 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain A residue 222 ILE 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 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 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 49 THR Chi-restraints excluded: chain D residue 206 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 418 TRP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 33 THR 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 156 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP 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 106 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 21 ILE 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: 6.9990 chunk 22 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 0.0070 chunk 92 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 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** ** 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** G 485 HIS H 34 HIS H 38 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.9761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17040 Z= 0.244 Angle : 0.791 14.083 23052 Z= 0.401 Chirality : 0.049 0.313 2511 Planarity : 0.006 0.107 3015 Dihedral : 9.290 110.524 2502 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.93 % Allowed : 23.98 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % 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: -3.90 (0.16), residues: 2106 helix: -1.41 (0.27), residues: 294 sheet: -2.76 (0.21), residues: 498 loop : -2.93 (0.14), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 409 HIS 0.005 0.001 HIS D 225 PHE 0.032 0.002 PHE A 93 TYR 0.018 0.002 TYR G 445 ARG 0.013 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 288 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 199 time to evaluate : 1.802 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 47 LYS cc_start: 0.6709 (ptpp) cc_final: 0.6313 (ptmm) REVERT: A 444 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6426 (tt) REVERT: A 447 ARG cc_start: 0.5715 (OUTLIER) cc_final: 0.3090 (ptt90) REVERT: A 465 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5540 (pp20) REVERT: A 467 PHE cc_start: 0.4474 (OUTLIER) cc_final: 0.4189 (m-80) REVERT: A 475 MET cc_start: 0.3974 (mmt) cc_final: 0.3753 (mpp) REVERT: A 493 MET cc_start: -0.1221 (mtt) cc_final: -0.3138 (ttm) REVERT: B 37 LYS cc_start: 0.8068 (tmmt) cc_final: 0.7554 (tmmt) REVERT: B 69 MET cc_start: 0.1837 (tpt) cc_final: 0.1087 (tpt) REVERT: B 93 TYR cc_start: 0.6839 (m-10) cc_final: 0.6406 (m-10) REVERT: C 37 MET cc_start: 0.6109 (tpt) cc_final: 0.5869 (tpt) REVERT: C 79 ILE cc_start: 0.3216 (OUTLIER) cc_final: 0.2783 (mp) REVERT: D 114 MET cc_start: 0.7389 (mmm) cc_final: 0.6708 (mtm) REVERT: E 80 MET cc_start: 0.5037 (tpt) cc_final: 0.4767 (tmm) REVERT: F 4 MET cc_start: 0.3162 (mmt) cc_final: 0.2871 (mmp) REVERT: F 49 ARG cc_start: 0.6953 (ptp-170) cc_final: 0.6511 (pmt170) REVERT: F 65 ARG cc_start: 0.2692 (OUTLIER) cc_final: 0.2289 (ppt170) REVERT: G 193 LEU cc_start: 0.6899 (mm) cc_final: 0.6592 (mp) REVERT: I 92 CYS cc_start: -0.0393 (OUTLIER) cc_final: -0.0927 (p) outliers start: 89 outliers final: 51 residues processed: 268 average time/residue: 1.0136 time to fit residues: 312.7550 Evaluate side-chains 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain A residue 222 ILE 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 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 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 31 THR Chi-restraints excluded: chain D residue 49 THR 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 310 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 385 THR 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 F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 33 THR 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 180 THR 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 332 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP 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 106 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 76 THR 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: 0.5980 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 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 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.9990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17040 Z= 0.244 Angle : 0.792 13.716 23052 Z= 0.399 Chirality : 0.049 0.308 2511 Planarity : 0.005 0.063 3015 Dihedral : 9.039 109.956 2502 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.49 % Allowed : 24.97 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 2.78 % 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: -3.76 (0.16), residues: 2106 helix: -1.33 (0.26), residues: 294 sheet: -2.70 (0.21), residues: 504 loop : -2.81 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 409 HIS 0.004 0.001 HIS F 38 PHE 0.029 0.002 PHE G 93 TYR 0.020 0.002 TYR G 445 ARG 0.012 0.001 ARG C 100 *********************** 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 269 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 188 time to evaluate : 1.918 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 343 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.3962 (tp) REVERT: A 444 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6172 (tt) REVERT: A 447 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.2876 (ptt90) REVERT: A 465 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5517 (pp20) REVERT: A 467 PHE cc_start: 0.4644 (OUTLIER) cc_final: 0.4375 (m-80) REVERT: A 493 MET cc_start: -0.1593 (mtt) cc_final: -0.3343 (ttm) REVERT: B 37 LYS cc_start: 0.7984 (tmmt) cc_final: 0.7509 (tmmt) REVERT: B 69 MET cc_start: 0.1758 (tpt) cc_final: 0.0969 (tpt) REVERT: B 93 TYR cc_start: 0.6960 (m-10) cc_final: 0.6592 (m-10) REVERT: C 37 MET cc_start: 0.6188 (tpt) cc_final: 0.5961 (tpt) REVERT: C 54 LEU cc_start: 0.2370 (OUTLIER) cc_final: 0.1605 (tp) REVERT: C 79 ILE cc_start: 0.3241 (OUTLIER) cc_final: 0.2830 (mp) REVERT: D 114 MET cc_start: 0.7376 (mmm) cc_final: 0.6791 (mtm) REVERT: E 42 LYS cc_start: 0.7355 (mmmt) cc_final: 0.6912 (pptt) REVERT: E 80 MET cc_start: 0.5101 (tpt) cc_final: 0.4829 (tmm) REVERT: F 65 ARG cc_start: 0.2739 (OUTLIER) cc_final: 0.2382 (ppt170) REVERT: F 79 ILE cc_start: 0.3047 (OUTLIER) cc_final: 0.2333 (mp) REVERT: G 193 LEU cc_start: 0.6938 (mm) cc_final: 0.6659 (mp) REVERT: G 255 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6100 (ttpp) REVERT: G 449 LYS cc_start: 0.4737 (mptt) cc_final: 0.4523 (mptt) REVERT: I 92 CYS cc_start: -0.0244 (OUTLIER) cc_final: -0.0596 (p) outliers start: 81 outliers final: 47 residues processed: 255 average time/residue: 1.0200 time to fit residues: 298.4262 Evaluate side-chains 224 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 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 444 LEU Chi-restraints excluded: chain A residue 447 ARG 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 106 TYR Chi-restraints excluded: chain C residue 54 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 31 THR Chi-restraints excluded: chain D residue 49 THR 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 344 ILE Chi-restraints excluded: chain D residue 385 THR 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 F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR 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 180 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 332 ILE 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 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 76 THR 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: 0.0170 chunk 191 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 0.3980 chunk 122 optimal weight: 6.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 225 HIS A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** 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 ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 1.0143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17040 Z= 0.231 Angle : 0.785 14.934 23052 Z= 0.393 Chirality : 0.049 0.187 2511 Planarity : 0.005 0.061 3015 Dihedral : 9.019 108.654 2502 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.04 % Allowed : 25.91 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 2.78 % 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: -1.15 (0.27), residues: 294 sheet: -2.58 (0.22), residues: 492 loop : -2.79 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 409 HIS 0.003 0.001 HIS D 9 PHE 0.028 0.002 PHE D 93 TYR 0.020 0.002 TYR G 445 ARG 0.007 0.001 ARG C 100 *********************** 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 253 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 180 time to evaluate : 1.830 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 343 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.3916 (tp) REVERT: A 444 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6147 (tt) REVERT: A 447 ARG cc_start: 0.5662 (OUTLIER) cc_final: 0.3158 (ptt90) REVERT: A 465 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5186 (pp20) REVERT: A 467 PHE cc_start: 0.4814 (OUTLIER) cc_final: 0.4487 (m-80) REVERT: A 493 MET cc_start: -0.1401 (mtt) cc_final: -0.3212 (ttm) REVERT: B 37 LYS cc_start: 0.7971 (tmmt) cc_final: 0.7566 (tmmt) REVERT: B 69 MET cc_start: 0.1845 (tpt) cc_final: 0.0968 (tpt) REVERT: B 93 TYR cc_start: 0.6992 (m-10) cc_final: 0.6560 (m-10) REVERT: C 54 LEU cc_start: 0.1701 (OUTLIER) cc_final: 0.1255 (tp) REVERT: C 79 ILE cc_start: 0.3184 (OUTLIER) cc_final: 0.2790 (mp) REVERT: D 9 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.6155 (p-80) REVERT: D 114 MET cc_start: 0.7310 (mmm) cc_final: 0.6753 (mtm) REVERT: D 452 LEU cc_start: 0.3995 (OUTLIER) cc_final: 0.3662 (tm) REVERT: E 42 LYS cc_start: 0.7432 (mmmt) cc_final: 0.6541 (mmtt) REVERT: E 80 MET cc_start: 0.5041 (tpt) cc_final: 0.4807 (tmm) REVERT: F 79 ILE cc_start: 0.3017 (OUTLIER) cc_final: 0.2336 (mp) REVERT: G 193 LEU cc_start: 0.6881 (mm) cc_final: 0.6656 (mp) REVERT: G 255 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.6022 (ttpp) REVERT: G 308 LEU cc_start: 0.5820 (pt) cc_final: 0.5501 (tp) REVERT: H 82 LEU cc_start: 0.5516 (mp) cc_final: 0.4806 (tp) REVERT: I 49 ARG cc_start: 0.6361 (ptt180) cc_final: 0.5976 (ppt170) outliers start: 73 outliers final: 42 residues processed: 236 average time/residue: 1.0748 time to fit residues: 289.9347 Evaluate side-chains 215 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 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 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 106 TYR Chi-restraints excluded: chain C residue 54 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 31 THR Chi-restraints excluded: chain D residue 49 THR 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 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 123 THR 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 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 I residue 13 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 387 GLN A 388 GLN A 481 ASN ** 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 314 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 54 ASN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 1.0378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17040 Z= 0.358 Angle : 0.886 14.591 23052 Z= 0.449 Chirality : 0.053 0.282 2511 Planarity : 0.006 0.078 3015 Dihedral : 9.659 113.454 2502 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 4.04 % Allowed : 26.41 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 2.78 % 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: -3.84 (0.16), residues: 2106 helix: -1.50 (0.26), residues: 306 sheet: -2.70 (0.21), residues: 522 loop : -2.86 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 409 HIS 0.008 0.002 HIS A 175 PHE 0.039 0.003 PHE A 464 TYR 0.044 0.003 TYR D 201 ARG 0.018 0.001 ARG G 131 ********************** 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 249 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 176 time to evaluate : 1.916 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 343 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.4028 (tp) REVERT: A 444 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6499 (tt) REVERT: A 447 ARG cc_start: 0.5734 (OUTLIER) cc_final: 0.3492 (ptt90) REVERT: A 467 PHE cc_start: 0.5264 (OUTLIER) cc_final: 0.4991 (m-80) REVERT: B 37 LYS cc_start: 0.7913 (tmmt) cc_final: 0.7513 (tmmt) REVERT: B 69 MET cc_start: 0.2122 (tpt) cc_final: 0.1239 (tpt) REVERT: B 93 TYR cc_start: 0.6957 (m-10) cc_final: 0.6623 (m-10) REVERT: C 79 ILE cc_start: 0.3230 (OUTLIER) cc_final: 0.2807 (mp) REVERT: D 452 LEU cc_start: 0.3963 (OUTLIER) cc_final: 0.3586 (tm) REVERT: E 42 LYS cc_start: 0.7388 (mmmt) cc_final: 0.6585 (mttp) REVERT: E 80 MET cc_start: 0.5652 (tpt) cc_final: 0.5267 (tmm) REVERT: F 79 ILE cc_start: 0.2801 (OUTLIER) cc_final: 0.2113 (mp) REVERT: G 193 LEU cc_start: 0.6899 (mm) cc_final: 0.6546 (mp) REVERT: H 42 LYS cc_start: 0.5735 (pptt) cc_final: 0.4977 (ttpt) REVERT: I 49 ARG cc_start: 0.6495 (ptt180) cc_final: 0.5935 (ppt170) REVERT: I 92 CYS cc_start: -0.0683 (OUTLIER) cc_final: -0.1107 (p) outliers start: 73 outliers final: 42 residues processed: 235 average time/residue: 1.0693 time to fit residues: 288.6946 Evaluate side-chains 216 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 148 THR 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 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 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 31 THR Chi-restraints excluded: chain D residue 49 THR 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 328 LEU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 156 MET 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 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 21 ILE 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: 0.7980 chunk 50 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 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** A 225 HIS 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** ** 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 ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.173029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.132568 restraints weight = 25014.288| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 3.18 r_work: 0.4417 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 1.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17040 Z= 0.263 Angle : 0.827 16.219 23052 Z= 0.414 Chirality : 0.050 0.256 2511 Planarity : 0.005 0.064 3015 Dihedral : 9.412 110.804 2502 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.16 % Allowed : 27.69 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 2.78 % 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: -3.69 (0.16), residues: 2106 helix: -1.15 (0.27), residues: 279 sheet: -2.55 (0.22), residues: 498 loop : -2.84 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 409 HIS 0.004 0.001 HIS D 275 PHE 0.039 0.003 PHE A 93 TYR 0.022 0.002 TYR D 201 ARG 0.014 0.001 ARG G 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6271.48 seconds wall clock time: 113 minutes 58.29 seconds (6838.29 seconds total)