Starting phenix.real_space_refine on Sun Aug 24 03:29:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv0_35735/08_2025/8iv0_35735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv0_35735/08_2025/8iv0_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 { model { file = "/net/cci-nas-00/data/ceres_data/8iv0_35735/08_2025/8iv0_35735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv0_35735/08_2025/8iv0_35735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iv0_35735/08_2025/8iv0_35735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv0_35735/08_2025/8iv0_35735.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.08, per 1000 atoms: 0.18 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=21, 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 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 463 " distance=2.04 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 463 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 269 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 269 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 67 " distance=2.02 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 67 " distance=2.02 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 88 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 273 " - pdb=" SG CYS D 297 " distance=2.03 Simple disulfide: pdb=" SG CYS G 273 " - pdb=" SG CYS G 297 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 474 " distance=2.03 Simple disulfide: pdb=" SG CYS G 470 " - pdb=" SG CYS G 474 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 552.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.54 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: 2.17 Time building geometry restraints manager: 1.15 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: 9276 16.50 - 32.99: 804 32.99 - 49.49: 162 49.49 - 65.99: 33 65.99 - 82.48: 21 Dihedral angle restraints: 10296 sinusoidal: 4224 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 10293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2148 0.093 - 0.186: 321 0.186 - 0.280: 30 0.280 - 0.373: 9 0.373 - 0.466: 3 Chirality restraints: 2511 Sorted by residual: chirality pdb=" CB ILE A 109 " pdb=" CA ILE A 109 " pdb=" CG1 ILE A 109 " pdb=" CG2 ILE A 109 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CB ILE G 109 " pdb=" CA ILE G 109 " pdb=" CG1 ILE G 109 " pdb=" CG2 ILE G 109 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CB ILE D 109 " pdb=" CA ILE D 109 " pdb=" CG1 ILE D 109 " pdb=" CG2 ILE D 109 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.41e+00 ... (remaining 2508 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 80 " 0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO C 81 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 80 " 0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO F 81 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 80 " -0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO I 81 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO I 81 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 81 " -0.046 5.00e-02 4.00e+02 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.75: 27 1.75 - 2.53: 267 2.53 - 3.32: 19463 3.32 - 4.11: 43105 4.11 - 4.90: 75703 Warning: very small nonbonded interaction distances. Nonbonded interactions: 138565 Sorted by model distance: nonbonded pdb=" CB SER A 198 " pdb=" NH2 ARG D 212 " model vdw 0.958 3.520 nonbonded pdb=" CB SER D 198 " pdb=" NH2 ARG G 212 " model vdw 0.958 3.520 nonbonded pdb=" NH2 ARG A 212 " pdb=" CB SER G 198 " model vdw 0.959 3.520 nonbonded pdb=" CB PRO A 213 " pdb=" CG2 THR G 234 " model vdw 0.990 3.860 nonbonded pdb=" CG2 THR A 234 " pdb=" CB PRO D 213 " model vdw 0.990 3.860 ... (remaining 138560 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: 0.02 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- 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 : 0.017 0.985 17076 Z= 1.558 Angle : 1.239 13.487 23121 Z= 0.672 Chirality : 0.069 0.466 2511 Planarity : 0.008 0.083 3015 Dihedral : 13.353 82.482 6363 Min Nonbonded Distance : 0.958 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.83 % Favored : 89.03 % Rotamer: Outliers : 0.66 % Allowed : 5.70 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 8.33 % Twisted General : 1.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG D 212 TYR 0.033 0.003 TYR D 201 PHE 0.033 0.005 PHE G 224 TRP 0.036 0.004 TRP G 347 HIS 0.007 0.002 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00651 (17040) covalent geometry : angle 1.23102 (23052) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.45719 ( 42) hydrogen bonds : bond 0.29182 ( 363) hydrogen bonds : angle 10.22914 ( 936) Misc. bond : bond 0.81427 ( 6) link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 4.16915 ( 27) *********************** 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 : 0.662 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: 0.4649 time to fit residues: 200.5465 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 : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** 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 264 GLN G 430 ASN ** G 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.191014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.151859 restraints weight = 24939.372| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 2.89 r_work: 0.4684 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17076 Z= 0.257 Angle : 0.976 15.727 23121 Z= 0.509 Chirality : 0.054 0.242 2511 Planarity : 0.014 0.366 3015 Dihedral : 9.811 69.866 2502 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 4.82 % Allowed : 14.17 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 8.33 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.14), residues: 2106 helix: -2.29 (0.24), residues: 288 sheet: -2.76 (0.22), residues: 438 loop : -3.61 (0.12), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.002 ARG A 212 TYR 0.029 0.003 TYR A 348 PHE 0.033 0.003 PHE G 224 TRP 0.034 0.003 TRP G 409 HIS 0.010 0.002 HIS G 225 Details of bonding type rmsd covalent geometry : bond 0.00556 (17040) covalent geometry : angle 0.96609 (23052) SS BOND : bond 0.00710 ( 21) SS BOND : angle 2.10491 ( 42) hydrogen bonds : bond 0.07483 ( 363) hydrogen bonds : angle 7.74203 ( 936) Misc. bond : bond 0.02048 ( 6) link_NAG-ASN : bond 0.01327 ( 9) link_NAG-ASN : angle 3.41481 ( 27) *********************** 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 368 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 281 time to evaluate : 0.485 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: 0.4488 (mmt) cc_final: 0.3870 (mpp) REVERT: B 37 LYS cc_start: 0.8352 (tttt) cc_final: 0.7951 (tmmt) REVERT: B 42 LYS cc_start: 0.6053 (mttm) cc_final: 0.5823 (mmtp) REVERT: B 63 PHE cc_start: 0.3307 (m-80) cc_final: 0.3097 (m-80) REVERT: B 69 MET cc_start: 0.1898 (OUTLIER) cc_final: 0.0976 (tpt) REVERT: B 80 MET cc_start: 0.4628 (tpt) cc_final: 0.4312 (tpt) REVERT: C 49 ARG cc_start: 0.6947 (ptp-170) cc_final: 0.6723 (ptp-170) REVERT: D 371 ILE cc_start: 0.6556 (tt) cc_final: 0.6278 (mt) REVERT: D 449 LYS cc_start: 0.4482 (mmpt) cc_final: 0.2762 (tptt) REVERT: D 493 MET cc_start: -0.0363 (mtt) cc_final: -0.0692 (mtt) REVERT: E 80 MET cc_start: 0.2973 (tpt) cc_final: 0.2764 (tmm) REVERT: G 156 MET cc_start: 0.4395 (mpt) cc_final: 0.3954 (mtt) REVERT: G 475 MET cc_start: 0.2206 (mpt) cc_final: 0.1926 (mpt) REVERT: H 33 MET cc_start: 0.5665 (ptt) cc_final: 0.4758 (tmm) REVERT: H 49 VAL cc_start: 0.3960 (p) cc_final: 0.3748 (t) REVERT: I 21 ILE cc_start: 0.2818 (OUTLIER) cc_final: 0.2428 (pt) outliers start: 87 outliers final: 21 residues processed: 340 average time/residue: 0.4368 time to fit residues: 168.7748 Evaluate side-chains 211 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 403 ILE 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 B residue 106 TYR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain D residue 31 THR 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 E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain I residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 137 optimal weight: 5.9990 chunk 172 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 147 ASN A 175 HIS A 225 HIS A 431 GLN A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 176 HIS ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN G 175 HIS G 176 HIS ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 GLN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.171430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.129858 restraints weight = 25587.478| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.98 r_work: 0.4388 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.8168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 17076 Z= 0.323 Angle : 1.038 15.091 23121 Z= 0.537 Chirality : 0.059 0.318 2511 Planarity : 0.009 0.232 3015 Dihedral : 9.675 64.341 2502 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.96 % Favored : 86.99 % Rotamer: Outliers : 6.81 % Allowed : 17.33 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 8.33 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.15), residues: 2106 helix: -2.24 (0.24), residues: 303 sheet: -2.84 (0.24), residues: 411 loop : -3.59 (0.13), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 212 TYR 0.036 0.003 TYR A 348 PHE 0.045 0.004 PHE D 464 TRP 0.024 0.003 TRP D 340 HIS 0.015 0.003 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00725 (17040) covalent geometry : angle 1.02196 (23052) SS BOND : bond 0.00556 ( 21) SS BOND : angle 2.25389 ( 42) hydrogen bonds : bond 0.07600 ( 363) hydrogen bonds : angle 7.78589 ( 936) Misc. bond : bond 0.01689 ( 6) link_NAG-ASN : bond 0.00831 ( 9) link_NAG-ASN : angle 4.72052 ( 27) *********************** 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 354 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 231 time to evaluate : 0.407 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 82 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6523 (mtp85) REVERT: A 104 ARG cc_start: 0.6371 (ptp-170) cc_final: 0.5763 (ttp-170) REVERT: A 193 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6414 (tt) REVERT: A 335 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.5482 (p90) REVERT: A 449 LYS cc_start: 0.5074 (mptt) cc_final: 0.4722 (mptt) REVERT: A 467 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.4055 (m-10) REVERT: A 475 MET cc_start: 0.4595 (mmt) cc_final: 0.3811 (mpp) REVERT: A 493 MET cc_start: 0.0065 (mtt) cc_final: -0.2478 (ttm) REVERT: B 37 LYS cc_start: 0.8423 (tttt) cc_final: 0.8066 (tmmt) REVERT: B 69 MET cc_start: 0.2693 (tpt) cc_final: 0.1833 (tpt) REVERT: C 79 ILE cc_start: 0.2932 (OUTLIER) cc_final: 0.2411 (mp) REVERT: D 4 ILE cc_start: 0.7160 (pt) cc_final: 0.6903 (pp) REVERT: D 114 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.6841 (mtm) REVERT: D 493 MET cc_start: 0.0433 (mtt) cc_final: 0.0086 (mtt) REVERT: E 3 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4834 (pp) REVERT: E 80 MET cc_start: 0.4354 (tpt) cc_final: 0.3591 (tmt) REVERT: G 36 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6169 (ptt90) REVERT: G 104 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5599 (mtm180) REVERT: G 386 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.6018 (p0) REVERT: G 464 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6883 (t80) REVERT: H 33 MET cc_start: 0.6322 (ptt) cc_final: 0.5374 (tmm) outliers start: 123 outliers final: 42 residues processed: 318 average time/residue: 0.4175 time to fit residues: 151.8289 Evaluate side-chains 241 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 212 ARG 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 381 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 386 ASN Chi-restraints excluded: chain G residue 440 GLU 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 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 195 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS G 264 GLN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.174395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.132832 restraints weight = 25474.607| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 2.95 r_work: 0.4426 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.8644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17076 Z= 0.206 Angle : 0.863 13.373 23121 Z= 0.441 Chirality : 0.052 0.249 2511 Planarity : 0.007 0.137 3015 Dihedral : 8.953 79.255 2502 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.59 % Allowed : 21.43 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.50 (0.15), residues: 2106 helix: -1.93 (0.25), residues: 300 sheet: -2.89 (0.23), residues: 435 loop : -3.48 (0.13), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 212 TYR 0.028 0.002 TYR D 201 PHE 0.034 0.003 PHE A 464 TRP 0.021 0.002 TRP G 409 HIS 0.008 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00460 (17040) covalent geometry : angle 0.84980 (23052) SS BOND : bond 0.00654 ( 21) SS BOND : angle 1.64175 ( 42) hydrogen bonds : bond 0.06318 ( 363) hydrogen bonds : angle 7.21808 ( 936) Misc. bond : bond 0.01604 ( 6) link_NAG-ASN : bond 0.00494 ( 9) link_NAG-ASN : angle 4.10187 ( 27) *********************** 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 314 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 213 time to evaluate : 0.614 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: 0.6846 (OUTLIER) cc_final: 0.6496 (mtp85) REVERT: A 104 ARG cc_start: 0.6275 (ptp-170) cc_final: 0.5622 (ttp-170) REVERT: A 449 LYS cc_start: 0.5019 (mptt) cc_final: 0.4637 (mptt) REVERT: A 475 MET cc_start: 0.4561 (mmt) cc_final: 0.4000 (mpp) REVERT: A 493 MET cc_start: -0.0212 (mtt) cc_final: -0.2655 (ttm) REVERT: B 37 LYS cc_start: 0.8397 (tttt) cc_final: 0.8029 (tmmt) REVERT: B 69 MET cc_start: 0.1818 (OUTLIER) cc_final: 0.0972 (tpt) REVERT: D 114 MET cc_start: 0.7587 (mmm) cc_final: 0.6765 (mtm) REVERT: D 493 MET cc_start: -0.0151 (mtt) cc_final: -0.0368 (mtt) REVERT: E 3 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4757 (pp) REVERT: E 80 MET cc_start: 0.4714 (tpt) cc_final: 0.4386 (tmm) REVERT: G 9 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.6342 (p-80) REVERT: G 104 ARG cc_start: 0.5494 (mtt180) cc_final: 0.5192 (mtm180) REVERT: H 33 MET cc_start: 0.6377 (ptt) cc_final: 0.5527 (tmm) REVERT: H 69 MET cc_start: 0.0721 (OUTLIER) cc_final: 0.0043 (pmm) outliers start: 101 outliers final: 43 residues processed: 290 average time/residue: 0.4224 time to fit residues: 140.1786 Evaluate side-chains 227 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 THR Chi-restraints excluded: chain A residue 212 ARG 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 381 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 76 THR 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 156 MET 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 276 SER Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 9 HIS 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 263 VAL Chi-restraints excluded: chain G residue 344 ILE 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 69 MET Chi-restraints excluded: chain H residue 106 TYR 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 6 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.165463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.126517 restraints weight = 25686.186| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 2.88 r_work: 0.4405 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.9116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17076 Z= 0.244 Angle : 0.901 13.772 23121 Z= 0.462 Chirality : 0.053 0.237 2511 Planarity : 0.006 0.073 3015 Dihedral : 8.931 89.255 2502 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.11 % Favored : 86.85 % Rotamer: Outliers : 6.31 % Allowed : 21.82 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 5.56 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.45 (0.15), residues: 2106 helix: -1.88 (0.25), residues: 300 sheet: -2.86 (0.23), residues: 441 loop : -3.45 (0.13), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 212 TYR 0.028 0.003 TYR D 201 PHE 0.039 0.003 PHE G 93 TRP 0.020 0.002 TRP G 409 HIS 0.009 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00554 (17040) covalent geometry : angle 0.88906 (23052) SS BOND : bond 0.00579 ( 21) SS BOND : angle 1.75805 ( 42) hydrogen bonds : bond 0.06176 ( 363) hydrogen bonds : angle 7.26437 ( 936) Misc. bond : bond 0.01253 ( 6) link_NAG-ASN : bond 0.00487 ( 9) link_NAG-ASN : angle 3.91694 ( 27) *********************** 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 308 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 194 time to evaluate : 0.624 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: 0.6827 (OUTLIER) cc_final: 0.6519 (mtp85) REVERT: A 104 ARG cc_start: 0.6554 (ptp-170) cc_final: 0.6187 (ttp-170) REVERT: A 193 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6569 (tt) REVERT: A 449 LYS cc_start: 0.4974 (mptt) cc_final: 0.4736 (mptt) REVERT: A 467 PHE cc_start: 0.4603 (OUTLIER) cc_final: 0.4376 (m-10) REVERT: A 493 MET cc_start: -0.0882 (mtt) cc_final: -0.2943 (ttm) REVERT: B 37 LYS cc_start: 0.8359 (tttt) cc_final: 0.7964 (tmmt) REVERT: B 69 MET cc_start: 0.2240 (tpt) cc_final: 0.1506 (tpt) REVERT: C 79 ILE cc_start: 0.3379 (OUTLIER) cc_final: 0.2915 (mp) REVERT: D 9 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.5471 (p-80) REVERT: D 114 MET cc_start: 0.7490 (mmm) cc_final: 0.6761 (mtm) REVERT: D 257 MET cc_start: 0.7067 (ptp) cc_final: 0.6814 (mtt) REVERT: E 3 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4733 (pp) REVERT: E 80 MET cc_start: 0.5160 (tpt) cc_final: 0.4831 (tmm) REVERT: F 79 ILE cc_start: 0.3295 (OUTLIER) cc_final: 0.2589 (tt) REVERT: G 9 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6486 (p-80) REVERT: G 104 ARG cc_start: 0.5697 (mtt180) cc_final: 0.5411 (mtm180) REVERT: G 447 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.5389 (tmm160) REVERT: H 33 MET cc_start: 0.6498 (ptt) cc_final: 0.5789 (tmm) REVERT: H 69 MET cc_start: 0.1181 (OUTLIER) cc_final: 0.0108 (pmm) outliers start: 114 outliers final: 54 residues processed: 279 average time/residue: 0.4182 time to fit residues: 133.8566 Evaluate side-chains 232 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 281 ILE 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 436 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 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 110 ASP 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 276 SER Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 37 THR 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 332 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 203 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 142 optimal weight: 0.0470 chunk 149 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.175440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.134362 restraints weight = 25101.394| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 2.91 r_work: 0.4460 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.9352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17076 Z= 0.166 Angle : 0.835 22.912 23121 Z= 0.421 Chirality : 0.050 0.275 2511 Planarity : 0.005 0.068 3015 Dihedral : 8.732 95.112 2502 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 4.93 % Allowed : 23.31 % Favored : 71.76 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.17 (0.15), residues: 2106 helix: -1.50 (0.27), residues: 294 sheet: -2.82 (0.21), residues: 504 loop : -3.22 (0.14), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 212 TYR 0.021 0.002 TYR H 26 PHE 0.031 0.003 PHE D 464 TRP 0.025 0.001 TRP G 409 HIS 0.007 0.001 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00368 (17040) covalent geometry : angle 0.80520 (23052) SS BOND : bond 0.00547 ( 21) SS BOND : angle 1.24830 ( 42) hydrogen bonds : bond 0.05417 ( 363) hydrogen bonds : angle 6.94902 ( 936) Misc. bond : bond 0.01228 ( 6) link_NAG-ASN : bond 0.01161 ( 9) link_NAG-ASN : angle 6.38972 ( 27) *********************** 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 287 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 198 time to evaluate : 0.440 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 104 ARG cc_start: 0.6450 (ptp-170) cc_final: 0.6020 (ttp-170) REVERT: A 156 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5440 (mmt) REVERT: A 343 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.3943 (tp) REVERT: A 449 LYS cc_start: 0.4932 (OUTLIER) cc_final: 0.4713 (mptt) REVERT: A 465 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5556 (tm-30) REVERT: A 493 MET cc_start: -0.0754 (mtt) cc_final: -0.2883 (ttm) REVERT: B 37 LYS cc_start: 0.8297 (tttt) cc_final: 0.7976 (tmmt) REVERT: B 46 TRP cc_start: 0.1671 (t60) cc_final: 0.1325 (t60) REVERT: B 69 MET cc_start: 0.1720 (OUTLIER) cc_final: 0.0973 (tpt) REVERT: C 79 ILE cc_start: 0.3313 (OUTLIER) cc_final: 0.2894 (mp) REVERT: D 114 MET cc_start: 0.7591 (mmm) cc_final: 0.6726 (mtm) REVERT: E 3 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4673 (pp) REVERT: E 80 MET cc_start: 0.5303 (tpt) cc_final: 0.5022 (tmm) REVERT: F 65 ARG cc_start: 0.2781 (OUTLIER) cc_final: 0.2259 (ppt170) REVERT: F 79 ILE cc_start: 0.3215 (OUTLIER) cc_final: 0.2481 (tt) REVERT: G 9 HIS cc_start: 0.6602 (OUTLIER) cc_final: 0.6199 (p-80) REVERT: G 36 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5998 (ptt180) REVERT: G 343 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4495 (mt) REVERT: G 447 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.5207 (tmm160) REVERT: H 33 MET cc_start: 0.6491 (ptt) cc_final: 0.5836 (tmm) REVERT: H 69 MET cc_start: 0.0838 (OUTLIER) cc_final: -0.0316 (pmm) REVERT: I 79 ILE cc_start: 0.5336 (OUTLIER) cc_final: 0.4791 (mt) outliers start: 89 outliers final: 41 residues processed: 269 average time/residue: 0.4072 time to fit residues: 124.9357 Evaluate side-chains 221 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 37 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 212 ARG 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 436 LEU Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 69 MET 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 49 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 276 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 36 ARG 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 332 ILE Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.165079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.125503 restraints weight = 25493.556| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 2.63 r_work: 0.4386 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.9717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17076 Z= 0.258 Angle : 0.972 25.577 23121 Z= 0.490 Chirality : 0.053 0.236 2511 Planarity : 0.006 0.066 3015 Dihedral : 9.247 106.506 2502 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 5.76 % Allowed : 23.64 % Favored : 70.60 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 5.56 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (0.15), residues: 2106 helix: -1.77 (0.25), residues: 303 sheet: -2.85 (0.22), residues: 462 loop : -3.28 (0.13), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 212 TYR 0.027 0.003 TYR D 89 PHE 0.042 0.003 PHE A 464 TRP 0.024 0.002 TRP G 409 HIS 0.010 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00581 (17040) covalent geometry : angle 0.93702 (23052) SS BOND : bond 0.00673 ( 21) SS BOND : angle 1.50107 ( 42) hydrogen bonds : bond 0.06303 ( 363) hydrogen bonds : angle 7.08089 ( 936) Misc. bond : bond 0.01288 ( 6) link_NAG-ASN : bond 0.01678 ( 9) link_NAG-ASN : angle 7.51219 ( 27) *********************** 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 292 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 188 time to evaluate : 0.652 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 47 LYS cc_start: 0.6816 (ptpp) cc_final: 0.6278 (ptmm) REVERT: A 82 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6531 (mtp85) REVERT: A 104 ARG cc_start: 0.6619 (ptp-170) cc_final: 0.6142 (ttp-170) REVERT: A 156 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5446 (mmt) REVERT: A 193 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6483 (tt) REVERT: A 343 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4170 (tp) REVERT: A 449 LYS cc_start: 0.5006 (OUTLIER) cc_final: 0.4734 (mptt) REVERT: A 467 PHE cc_start: 0.5169 (OUTLIER) cc_final: 0.4823 (m-80) REVERT: A 493 MET cc_start: -0.0860 (mtt) cc_final: -0.2928 (ttm) REVERT: B 37 LYS cc_start: 0.8276 (tttt) cc_final: 0.8020 (tmmt) REVERT: B 46 TRP cc_start: 0.2076 (t60) cc_final: 0.1589 (t60) REVERT: B 69 MET cc_start: 0.2465 (OUTLIER) cc_final: 0.1583 (tpt) REVERT: C 79 ILE cc_start: 0.3312 (OUTLIER) cc_final: 0.2820 (mp) REVERT: D 114 MET cc_start: 0.7498 (mmm) cc_final: 0.6802 (mtm) REVERT: E 3 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4858 (pt) REVERT: E 80 MET cc_start: 0.5632 (tpt) cc_final: 0.5310 (tmm) REVERT: G 36 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5899 (ptp-170) REVERT: G 104 ARG cc_start: 0.6043 (mtm180) cc_final: 0.5727 (mtm180) REVERT: G 299 ARG cc_start: 0.5742 (OUTLIER) cc_final: 0.3797 (mpp80) REVERT: G 447 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.5485 (tmm160) REVERT: G 493 MET cc_start: -0.1224 (OUTLIER) cc_final: -0.1595 (mtt) REVERT: H 33 MET cc_start: 0.6601 (ptt) cc_final: 0.6129 (tmm) REVERT: I 79 ILE cc_start: 0.5051 (OUTLIER) cc_final: 0.4554 (mp) outliers start: 104 outliers final: 47 residues processed: 264 average time/residue: 0.4336 time to fit residues: 130.5491 Evaluate side-chains 235 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 37 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 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 110 ASP 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 276 SER 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 D residue 452 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 110 ASP 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 299 ARG Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 493 MET Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 80 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 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 388 GLN B 38 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.169990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.129892 restraints weight = 24971.583| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 2.95 r_work: 0.4442 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.9910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17076 Z= 0.182 Angle : 0.863 15.747 23121 Z= 0.432 Chirality : 0.052 0.692 2511 Planarity : 0.005 0.066 3015 Dihedral : 8.553 107.767 2502 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 4.82 % Allowed : 24.81 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.09 (0.15), residues: 2106 helix: -1.49 (0.26), residues: 294 sheet: -2.77 (0.21), residues: 513 loop : -3.14 (0.14), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 212 TYR 0.017 0.002 TYR G 89 PHE 0.034 0.002 PHE D 464 TRP 0.055 0.002 TRP E 46 HIS 0.009 0.002 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00406 (17040) covalent geometry : angle 0.83955 (23052) SS BOND : bond 0.00514 ( 21) SS BOND : angle 1.96255 ( 42) hydrogen bonds : bond 0.05568 ( 363) hydrogen bonds : angle 6.91821 ( 936) Misc. bond : bond 0.01236 ( 6) link_NAG-ASN : bond 0.01131 ( 9) link_NAG-ASN : angle 5.46050 ( 27) *********************** 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 272 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 185 time to evaluate : 0.440 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: 0.6862 (ptpp) cc_final: 0.6316 (ptmm) REVERT: A 82 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6498 (mtp85) REVERT: A 104 ARG cc_start: 0.6427 (ptp-170) cc_final: 0.6093 (ttp-170) REVERT: A 156 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5298 (mmt) REVERT: A 343 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4076 (tp) REVERT: A 351 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6076 (ttm110) REVERT: A 449 LYS cc_start: 0.5032 (OUTLIER) cc_final: 0.4790 (mptt) REVERT: A 467 PHE cc_start: 0.4961 (OUTLIER) cc_final: 0.4642 (m-80) REVERT: B 37 LYS cc_start: 0.8247 (tttt) cc_final: 0.7972 (tmmt) REVERT: B 69 MET cc_start: 0.1825 (OUTLIER) cc_final: 0.0995 (tpt) REVERT: C 79 ILE cc_start: 0.3198 (OUTLIER) cc_final: 0.2795 (mp) REVERT: D 47 LYS cc_start: 0.7018 (ptpp) cc_final: 0.6798 (ptmm) REVERT: D 114 MET cc_start: 0.7428 (mmm) cc_final: 0.6748 (mtm) REVERT: E 3 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4683 (pt) REVERT: E 42 LYS cc_start: 0.7554 (mmmt) cc_final: 0.7020 (pptt) REVERT: E 80 MET cc_start: 0.5576 (tpt) cc_final: 0.5330 (tmm) REVERT: F 49 ARG cc_start: 0.7198 (ptp-170) cc_final: 0.6902 (pmt170) REVERT: F 65 ARG cc_start: 0.2924 (OUTLIER) cc_final: 0.2498 (ppt170) REVERT: F 79 ILE cc_start: 0.3035 (OUTLIER) cc_final: 0.2280 (mp) REVERT: G 36 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5693 (ptp-170) REVERT: G 447 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.5216 (tmm160) REVERT: G 449 LYS cc_start: 0.5334 (mptt) cc_final: 0.5091 (mptt) REVERT: H 33 MET cc_start: 0.6482 (ptt) cc_final: 0.6082 (tmm) REVERT: I 79 ILE cc_start: 0.4805 (OUTLIER) cc_final: 0.4373 (mp) outliers start: 87 outliers final: 46 residues processed: 258 average time/residue: 0.4366 time to fit residues: 128.2701 Evaluate side-chains 229 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 37 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 212 ARG 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 351 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 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 110 ASP 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 252 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP 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 F residue 92 CYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain 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 79 ILE Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 119 ASN E 34 HIS ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.173512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.132658 restraints weight = 25169.653| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 2.91 r_work: 0.4418 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 1.0055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17076 Z= 0.181 Angle : 0.851 15.340 23121 Z= 0.426 Chirality : 0.051 0.501 2511 Planarity : 0.005 0.065 3015 Dihedral : 8.940 107.389 2502 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 4.93 % Allowed : 25.03 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.98 (0.16), residues: 2106 helix: -1.40 (0.26), residues: 294 sheet: -2.65 (0.23), residues: 450 loop : -3.10 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 212 TYR 0.018 0.002 TYR G 89 PHE 0.032 0.002 PHE D 464 TRP 0.028 0.002 TRP G 409 HIS 0.011 0.002 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00411 (17040) covalent geometry : angle 0.83127 (23052) SS BOND : bond 0.00584 ( 21) SS BOND : angle 2.12014 ( 42) hydrogen bonds : bond 0.05393 ( 363) hydrogen bonds : angle 6.86023 ( 936) Misc. bond : bond 0.01224 ( 6) link_NAG-ASN : bond 0.00603 ( 9) link_NAG-ASN : angle 4.81627 ( 27) *********************** 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 267 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 178 time to evaluate : 0.696 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: 0.6856 (ptpp) cc_final: 0.6279 (ptmm) REVERT: A 82 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6500 (mtp85) REVERT: A 104 ARG cc_start: 0.6355 (ptp-170) cc_final: 0.5992 (ttp-170) REVERT: A 343 LEU cc_start: 0.4717 (OUTLIER) cc_final: 0.3967 (tp) REVERT: A 449 LYS cc_start: 0.4995 (OUTLIER) cc_final: 0.4753 (mptt) REVERT: A 465 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5453 (pp20) REVERT: A 467 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.5004 (m-80) REVERT: B 37 LYS cc_start: 0.8132 (tttt) cc_final: 0.7879 (tmmt) REVERT: B 69 MET cc_start: 0.1744 (tpt) cc_final: 0.0941 (tpt) REVERT: C 79 ILE cc_start: 0.3292 (OUTLIER) cc_final: 0.2871 (mp) REVERT: D 47 LYS cc_start: 0.6919 (ptpp) cc_final: 0.6350 (ptmm) REVERT: D 114 MET cc_start: 0.7648 (mmm) cc_final: 0.6795 (mtm) REVERT: E 3 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4652 (pt) REVERT: E 47 ILE cc_start: 0.4458 (pt) cc_final: 0.4166 (pp) REVERT: E 80 MET cc_start: 0.5546 (tpt) cc_final: 0.5324 (tmm) REVERT: F 49 ARG cc_start: 0.7210 (ptp-170) cc_final: 0.6827 (pmt170) REVERT: F 65 ARG cc_start: 0.2819 (OUTLIER) cc_final: 0.2389 (ppt170) REVERT: F 79 ILE cc_start: 0.3093 (OUTLIER) cc_final: 0.2371 (mp) REVERT: G 36 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5826 (ptt180) REVERT: G 89 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.5903 (m-80) REVERT: G 447 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5488 (tmm160) REVERT: G 449 LYS cc_start: 0.5354 (mptt) cc_final: 0.5121 (mptt) REVERT: H 33 MET cc_start: 0.6449 (ptt) cc_final: 0.5931 (tmm) REVERT: H 69 MET cc_start: 0.0543 (ppp) cc_final: -0.0370 (pmm) REVERT: H 82 LEU cc_start: 0.5882 (mp) cc_final: 0.5222 (tp) outliers start: 89 outliers final: 48 residues processed: 249 average time/residue: 0.5606 time to fit residues: 157.9103 Evaluate side-chains 224 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 312 MET 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 436 LEU Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET 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 101 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU 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 F residue 92 CYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG 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 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 0.0980 chunk 154 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 HIS ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** 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 = 0.5074 r_free = 0.5074 target = 0.175314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.134613 restraints weight = 24877.674| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 2.88 r_work: 0.4439 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 1.0222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17076 Z= 0.170 Angle : 0.834 15.123 23121 Z= 0.417 Chirality : 0.051 0.442 2511 Planarity : 0.005 0.065 3015 Dihedral : 8.824 106.481 2502 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.93 % Allowed : 26.02 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.16), residues: 2106 helix: -1.35 (0.27), residues: 294 sheet: -2.69 (0.21), residues: 513 loop : -3.05 (0.14), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 100 TYR 0.019 0.002 TYR D 274 PHE 0.034 0.002 PHE D 464 TRP 0.043 0.002 TRP A 409 HIS 0.011 0.002 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00386 (17040) covalent geometry : angle 0.81688 (23052) SS BOND : bond 0.00567 ( 21) SS BOND : angle 1.88328 ( 42) hydrogen bonds : bond 0.05172 ( 363) hydrogen bonds : angle 6.84551 ( 936) Misc. bond : bond 0.01212 ( 6) link_NAG-ASN : bond 0.00733 ( 9) link_NAG-ASN : angle 4.58002 ( 27) ********************** 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 250 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 179 time to evaluate : 0.679 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 47 LYS cc_start: 0.6855 (ptpp) cc_final: 0.6283 (ptmm) REVERT: A 82 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6453 (mtp85) REVERT: A 104 ARG cc_start: 0.6265 (ptp-170) cc_final: 0.5929 (ttp-170) REVERT: A 343 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4007 (tp) REVERT: A 449 LYS cc_start: 0.4972 (OUTLIER) cc_final: 0.4744 (mptt) REVERT: A 465 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5049 (pp20) REVERT: A 467 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: B 37 LYS cc_start: 0.8082 (tttt) cc_final: 0.7778 (tmmt) REVERT: B 69 MET cc_start: 0.1704 (OUTLIER) cc_final: 0.0901 (tpt) REVERT: B 93 TYR cc_start: 0.7218 (m-10) cc_final: 0.6727 (m-10) REVERT: C 79 ILE cc_start: 0.3253 (OUTLIER) cc_final: 0.2820 (mp) REVERT: D 45 LYS cc_start: 0.7083 (tmmt) cc_final: 0.6661 (ttmt) REVERT: D 47 LYS cc_start: 0.6913 (ptpp) cc_final: 0.6336 (ptmm) REVERT: D 114 MET cc_start: 0.7604 (mmm) cc_final: 0.6766 (mtm) REVERT: E 3 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4813 (pt) REVERT: E 42 LYS cc_start: 0.7504 (mmmt) cc_final: 0.6997 (pptt) REVERT: E 47 ILE cc_start: 0.4771 (pt) cc_final: 0.4434 (pp) REVERT: F 4 MET cc_start: 0.2090 (mmt) cc_final: 0.1551 (mmp) REVERT: F 49 ARG cc_start: 0.7158 (ptp-170) cc_final: 0.6798 (pmt170) REVERT: F 65 ARG cc_start: 0.2719 (OUTLIER) cc_final: 0.2231 (ppt170) REVERT: F 79 ILE cc_start: 0.2922 (OUTLIER) cc_final: 0.2226 (mp) REVERT: G 36 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5829 (ptt180) REVERT: G 89 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: G 392 ILE cc_start: 0.5603 (pt) cc_final: 0.5212 (tp) REVERT: G 447 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.5477 (tmm160) REVERT: G 449 LYS cc_start: 0.5303 (mptt) cc_final: 0.5080 (mptt) REVERT: H 33 MET cc_start: 0.6405 (ptt) cc_final: 0.5983 (tmm) REVERT: H 69 MET cc_start: 0.0419 (ppp) cc_final: -0.0607 (pmm) REVERT: H 82 LEU cc_start: 0.5831 (mp) cc_final: 0.5186 (tp) REVERT: I 92 CYS cc_start: -0.0709 (OUTLIER) cc_final: -0.1168 (p) outliers start: 71 outliers final: 44 residues processed: 235 average time/residue: 0.5655 time to fit residues: 150.0614 Evaluate side-chains 223 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU 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 F residue 92 CYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG 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 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 121 optimal weight: 0.1980 chunk 202 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 191 optimal weight: 0.0270 chunk 131 optimal weight: 7.9990 chunk 6 optimal weight: 0.0070 chunk 172 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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 387 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 485 HIS ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.180079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.139961 restraints weight = 24912.903| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 2.90 r_work: 0.4511 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 1.0444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17076 Z= 0.145 Angle : 0.807 14.683 23121 Z= 0.402 Chirality : 0.049 0.389 2511 Planarity : 0.005 0.065 3015 Dihedral : 8.539 102.379 2502 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.54 % Allowed : 26.74 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.16), residues: 2106 helix: -1.15 (0.27), residues: 303 sheet: -2.49 (0.22), residues: 486 loop : -2.98 (0.14), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 212 TYR 0.015 0.002 TYR G 138 PHE 0.035 0.002 PHE D 464 TRP 0.041 0.002 TRP A 409 HIS 0.011 0.001 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00326 (17040) covalent geometry : angle 0.79234 (23052) SS BOND : bond 0.00467 ( 21) SS BOND : angle 1.62796 ( 42) hydrogen bonds : bond 0.04670 ( 363) hydrogen bonds : angle 6.64900 ( 936) Misc. bond : bond 0.01194 ( 6) link_NAG-ASN : bond 0.00752 ( 9) link_NAG-ASN : angle 4.26639 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5840.20 seconds wall clock time: 100 minutes 25.44 seconds (6025.44 seconds total)