Starting phenix.real_space_refine on Sat Jun 14 23:29:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv0_35735/06_2025/8iv0_35735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv0_35735/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv0_35735/06_2025/8iv0_35735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv0_35735/06_2025/8iv0_35735.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv0_35735/06_2025/8iv0_35735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv0_35735/06_2025/8iv0_35735.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10386 2.51 5 N 2919 2.21 5 O 3306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16701 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 904 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 10.05, per 1000 atoms: 0.60 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: 4.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 48 sheets defined 18.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.789A pdb=" N THR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 4.059A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.822A pdb=" N ARG A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 400 through 450 removed outlier: 5.010A pdb=" N GLU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.084A pdb=" N MET A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.546A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.890A pdb=" N LYS B 66 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 67' Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.587A pdb=" N SER B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.556A pdb=" N ASP C 86 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.788A pdb=" N THR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 4.059A pdb=" N LEU D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 106 removed outlier: 4.822A pdb=" N ARG D 104 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 400 through 450 removed outlier: 5.010A pdb=" N GLU D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG D 447 " --> pdb=" O LYS D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.085A pdb=" N MET D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 removed outlier: 3.547A pdb=" N MET D 493 " --> pdb=" O ARG D 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.890A pdb=" N LYS E 66 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA E 67 " --> pdb=" O LYS E 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 67' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.587A pdb=" N SER E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.557A pdb=" N ASP F 86 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 87 " --> pdb=" O GLU F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 87' Processing helix chain 'G' and resid 58 through 63 removed outlier: 3.788A pdb=" N THR G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 4.059A pdb=" N LEU G 71 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 100 Processing helix chain 'G' and resid 101 through 106 removed outlier: 4.821A pdb=" N ARG G 104 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 382 Processing helix chain 'G' and resid 400 through 450 removed outlier: 5.010A pdb=" N GLU G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET G 441 " --> pdb=" O ALA G 437 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP G 442 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG G 447 " --> pdb=" O LYS G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 456 Processing helix chain 'G' and resid 471 through 479 removed outlier: 4.084A pdb=" N MET G 475 " --> pdb=" O ASP G 471 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 493 removed outlier: 3.546A pdb=" N MET G 493 " --> pdb=" O ARG G 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.891A pdb=" N LYS H 66 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA H 67 " --> pdb=" O LYS H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 67' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.586A pdb=" N SER H 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.557A pdb=" N ASP I 86 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA I 87 " --> pdb=" O GLU I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing sheet with id=1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.885A pdb=" N GLY A 7 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 349 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS A 352 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=3, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.715A pdb=" N LEU A 308 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=5, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.555A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=7, first strand: chain 'A' and resid 111 through 113 Processing sheet with id=8, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.542A pdb=" N ALA A 245 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 174 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 223 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.647A pdb=" N THR A 236 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 197 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.988A pdb=" N VAL A 294 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=12, first strand: chain 'B' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR B 114 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 111 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 93 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 113 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 92 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR B 114 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 111 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 93 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 113 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 106 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=15, first strand: chain 'C' and resid 5 through 6 removed outlier: 4.232A pdb=" N ILE C 21 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 77 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 23 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 75 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 76 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.858A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.885A pdb=" N GLY D 7 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 349 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS D 352 " --> pdb=" O GLY D 359 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY D 359 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=19, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.714A pdb=" N LEU D 308 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=21, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.555A pdb=" N ILE D 42 " --> pdb=" O ASP D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=23, first strand: chain 'D' and resid 111 through 113 Processing sheet with id=24, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.542A pdb=" N ALA D 245 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 174 " --> pdb=" O ASP D 223 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP D 223 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'D' and resid 156 through 160 removed outlier: 3.647A pdb=" N THR D 236 " --> pdb=" O GLY D 197 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 197 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 273 through 274 removed outlier: 3.989A pdb=" N VAL D 294 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=28, first strand: chain 'E' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL E 11 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 114 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR E 93 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 113 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 92 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL E 11 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 114 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR E 93 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 113 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR E 106 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=31, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.231A pdb=" N ILE F 21 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU F 77 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR F 23 " --> pdb=" O PHE F 75 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE F 75 " --> pdb=" O TYR F 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 76 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'F' and resid 39 through 41 removed outlier: 6.858A pdb=" N TRP F 39 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.885A pdb=" N GLY G 7 " --> pdb=" O GLY G 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY G 349 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS G 352 " --> pdb=" O GLY G 359 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY G 359 " --> pdb=" O HIS G 352 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=35, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.715A pdb=" N LEU G 308 " --> pdb=" O THR G 31 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=37, first strand: chain 'G' and resid 42 through 43 removed outlier: 5.555A pdb=" N ILE G 42 " --> pdb=" O ASP G 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=37 Processing sheet with id=38, first strand: chain 'G' and resid 49 through 51 Processing sheet with id=39, first strand: chain 'G' and resid 111 through 113 Processing sheet with id=40, first strand: chain 'G' and resid 141 through 143 removed outlier: 3.542A pdb=" N ALA G 245 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE G 174 " --> pdb=" O ASP G 223 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP G 223 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 156 through 160 removed outlier: 3.647A pdb=" N THR G 236 " --> pdb=" O GLY G 197 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 197 " --> pdb=" O THR G 236 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'G' and resid 273 through 274 removed outlier: 3.988A pdb=" N VAL G 294 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=44, first strand: chain 'H' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL H 11 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR H 114 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR H 93 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 113 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE H 92 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'H' and resid 10 through 11 removed outlier: 9.093A pdb=" N VAL H 11 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR H 114 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR H 93 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 113 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR H 106 " --> pdb=" O ILE H 97 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=47, first strand: chain 'I' and resid 5 through 6 removed outlier: 4.232A pdb=" N ILE I 21 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU I 77 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR I 23 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE I 75 " --> pdb=" O TYR I 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR I 76 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.859A pdb=" N TRP I 39 " --> pdb=" O LEU I 51 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 4.82 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:14.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.13), residues: 2106 helix: -2.70 (0.25), residues: 288 sheet: -3.40 (0.19), residues: 441 loop : -3.90 (0.11), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP G 347 HIS 0.007 0.002 HIS D 9 PHE 0.033 0.005 PHE G 224 TYR 0.033 0.003 TYR D 201 ARG 0.010 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 4.16915 ( 27) hydrogen bonds : bond 0.29182 ( 363) hydrogen bonds : angle 10.22914 ( 936) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.45719 ( 42) covalent geometry : bond 0.00651 (17040) covalent geometry : angle 1.23102 (23052) Misc. bond : bond 0.81427 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 374 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.6543 (mp) cc_final: 0.6121 (mt) REVERT: B 93 TYR cc_start: 0.7027 (m-10) cc_final: 0.6656 (m-10) REVERT: C 41 GLN cc_start: 0.5431 (tt0) cc_final: 0.4978 (tt0) REVERT: E 93 TYR cc_start: 0.4819 (m-10) cc_final: 0.4611 (m-80) REVERT: G 156 MET cc_start: 0.2299 (mpt) cc_final: 0.1726 (mtt) REVERT: G 343 LEU cc_start: 0.3177 (mm) cc_final: 0.2900 (mt) outliers start: 12 outliers final: 0 residues processed: 383 average time/residue: 1.1782 time to fit residues: 509.0359 Evaluate side-chains 183 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN A 176 HIS A 388 GLN A 421 ASN A 430 ASN A 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 202 GLN D 405 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 485 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 405 ASN G 430 ASN ** G 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN G 485 HIS ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5324 r_free = 0.5324 target = 0.199582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.162151 restraints weight = 25114.311| |-----------------------------------------------------------------------------| r_work (start): 0.4894 rms_B_bonded: 2.87 r_work: 0.4806 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17076 Z= 0.230 Angle : 0.931 17.668 23121 Z= 0.483 Chirality : 0.054 0.353 2511 Planarity : 0.013 0.352 3015 Dihedral : 9.395 61.288 2502 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 4.43 % Allowed : 14.06 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 8.33 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.14), residues: 2106 helix: -2.05 (0.25), residues: 270 sheet: -2.76 (0.21), residues: 459 loop : -3.57 (0.12), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 409 HIS 0.008 0.002 HIS D 485 PHE 0.028 0.003 PHE G 224 TYR 0.028 0.003 TYR D 274 ARG 0.043 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.01429 ( 9) link_NAG-ASN : angle 3.41314 ( 27) hydrogen bonds : bond 0.07000 ( 363) hydrogen bonds : angle 7.49905 ( 936) SS BOND : bond 0.00678 ( 21) SS BOND : angle 1.83015 ( 42) covalent geometry : bond 0.00487 (17040) covalent geometry : angle 0.92188 (23052) Misc. bond : bond 0.02401 ( 6) *********************** 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 366 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 286 time to evaluate : 1.735 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 313 LYS cc_start: 0.5307 (OUTLIER) cc_final: 0.5082 (tptm) REVERT: A 475 MET cc_start: 0.4249 (mmt) cc_final: 0.3666 (mpp) REVERT: B 37 LYS cc_start: 0.8393 (tttt) cc_final: 0.7913 (tmmt) REVERT: B 42 LYS cc_start: 0.6092 (mttm) cc_final: 0.5838 (mmtp) REVERT: B 69 MET cc_start: 0.1671 (OUTLIER) cc_final: 0.0817 (tpt) REVERT: B 80 MET cc_start: 0.4568 (tpt) cc_final: 0.4189 (tpt) REVERT: D 449 LYS cc_start: 0.4175 (mmpt) cc_final: 0.2900 (tptt) REVERT: E 80 MET cc_start: 0.2842 (tpt) cc_final: 0.2478 (tmm) REVERT: G 156 MET cc_start: 0.4156 (mpt) cc_final: 0.3588 (mtt) REVERT: G 257 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.4290 (pmm) REVERT: G 475 MET cc_start: 0.2304 (mpt) cc_final: 0.1940 (mpt) outliers start: 80 outliers final: 24 residues processed: 339 average time/residue: 1.1424 time to fit residues: 437.8249 Evaluate side-chains 215 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 313 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 480 ASN Chi-restraints excluded: chain H residue 3 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 64 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 0.0030 chunk 97 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS A 432 HIS ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.190744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.150737 restraints weight = 24994.978| |-----------------------------------------------------------------------------| r_work (start): 0.4763 rms_B_bonded: 2.94 r_work: 0.4666 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17076 Z= 0.183 Angle : 0.857 14.067 23121 Z= 0.437 Chirality : 0.050 0.239 2511 Planarity : 0.007 0.198 3015 Dihedral : 10.378 178.779 2502 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 4.93 % Allowed : 18.11 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 5.56 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.15), residues: 2106 helix: -1.80 (0.25), residues: 288 sheet: -2.81 (0.20), residues: 498 loop : -3.35 (0.13), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 340 HIS 0.007 0.001 HIS F 80 PHE 0.026 0.002 PHE G 116 TYR 0.017 0.002 TYR D 364 ARG 0.017 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 9) link_NAG-ASN : angle 3.36888 ( 27) hydrogen bonds : bond 0.06176 ( 363) hydrogen bonds : angle 7.02949 ( 936) SS BOND : bond 0.00366 ( 21) SS BOND : angle 2.13978 ( 42) covalent geometry : bond 0.00404 (17040) covalent geometry : angle 0.84535 (23052) Misc. bond : bond 0.01489 ( 6) *********************** 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 309 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 1.667 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 475 MET cc_start: 0.4270 (mmt) cc_final: 0.3859 (mpp) REVERT: A 493 MET cc_start: -0.0068 (mtt) cc_final: -0.2545 (ttm) REVERT: B 37 LYS cc_start: 0.8361 (tttt) cc_final: 0.8021 (tmmt) REVERT: C 49 ARG cc_start: 0.6468 (ptp-170) cc_final: 0.6241 (pmt170) REVERT: C 74 ASP cc_start: 0.0857 (m-30) cc_final: 0.0616 (t0) REVERT: D 425 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6305 (pp) REVERT: D 452 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2612 (tm) REVERT: E 3 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.4640 (pp) REVERT: E 69 MET cc_start: -0.0124 (tpt) cc_final: -0.1700 (pp-130) REVERT: E 80 MET cc_start: 0.3085 (tpt) cc_final: 0.2500 (tmm) REVERT: G 465 GLU cc_start: 0.4919 (OUTLIER) cc_final: 0.4632 (tm-30) REVERT: H 33 MET cc_start: 0.5256 (OUTLIER) cc_final: 0.4260 (tmm) outliers start: 89 outliers final: 30 residues processed: 290 average time/residue: 0.9822 time to fit residues: 326.4752 Evaluate side-chains 218 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 461 THR 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 G residue 33 THR Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 225 HIS A 432 HIS A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN G 314 ASN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.172249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.130983 restraints weight = 25439.778| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 2.93 r_work: 0.4406 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 17076 Z= 0.313 Angle : 1.018 17.001 23121 Z= 0.523 Chirality : 0.058 0.391 2511 Planarity : 0.008 0.116 3015 Dihedral : 10.918 166.466 2502 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 6.20 % Allowed : 19.71 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.15), residues: 2106 helix: -1.95 (0.25), residues: 291 sheet: -3.04 (0.24), residues: 402 loop : -3.38 (0.13), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 340 HIS 0.014 0.003 HIS D 275 PHE 0.047 0.004 PHE A 464 TYR 0.040 0.003 TYR D 201 ARG 0.032 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 9) link_NAG-ASN : angle 3.50314 ( 27) hydrogen bonds : bond 0.06830 ( 363) hydrogen bonds : angle 7.49138 ( 936) SS BOND : bond 0.00839 ( 21) SS BOND : angle 2.35695 ( 42) covalent geometry : bond 0.00701 (17040) covalent geometry : angle 1.00724 (23052) Misc. bond : bond 0.01950 ( 6) *********************** 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 341 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 229 time to evaluate : 1.921 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: 0.6823 (OUTLIER) cc_final: 0.6541 (mtp85) REVERT: A 193 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6425 (tt) REVERT: A 335 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.5362 (p90) REVERT: A 387 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6737 (tm-30) REVERT: A 449 LYS cc_start: 0.4908 (mptt) cc_final: 0.4586 (mptt) REVERT: A 493 MET cc_start: -0.0097 (mtt) cc_final: -0.2548 (ttm) REVERT: B 34 HIS cc_start: 0.6134 (OUTLIER) cc_final: 0.5915 (m-70) REVERT: B 37 LYS cc_start: 0.8403 (tttt) cc_final: 0.8035 (tmmt) REVERT: B 69 MET cc_start: 0.2219 (tpt) cc_final: 0.1652 (tpt) REVERT: C 49 ARG cc_start: 0.7066 (ptp-170) cc_final: 0.6808 (ptp-170) REVERT: D 104 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6263 (ptt180) REVERT: D 114 MET cc_start: 0.7508 (mmm) cc_final: 0.6878 (mtm) REVERT: E 3 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4990 (pp) REVERT: E 80 MET cc_start: 0.4333 (tpt) cc_final: 0.3530 (tmt) REVERT: G 388 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: G 465 GLU cc_start: 0.5347 (OUTLIER) cc_final: 0.5027 (tm-30) REVERT: H 33 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5344 (tmm) REVERT: I 44 PRO cc_start: 0.7164 (Cg_endo) cc_final: 0.6894 (Cg_exo) outliers start: 112 outliers final: 44 residues processed: 314 average time/residue: 1.1789 time to fit residues: 422.2969 Evaluate side-chains 233 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 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 49 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 388 GLN Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 126 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 142 optimal weight: 0.4980 chunk 137 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS G 264 GLN G 388 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.178547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.137331 restraints weight = 25342.596| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 2.95 r_work: 0.4490 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.8782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17076 Z= 0.165 Angle : 0.824 13.941 23121 Z= 0.419 Chirality : 0.049 0.245 2511 Planarity : 0.006 0.111 3015 Dihedral : 10.387 176.037 2502 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.87 % Allowed : 22.92 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.15), residues: 2106 helix: -1.66 (0.26), residues: 288 sheet: -3.07 (0.21), residues: 468 loop : -3.16 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 340 HIS 0.008 0.001 HIS F 80 PHE 0.034 0.003 PHE D 93 TYR 0.015 0.002 TYR C 91 ARG 0.010 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 9) link_NAG-ASN : angle 3.18137 ( 27) hydrogen bonds : bond 0.05506 ( 363) hydrogen bonds : angle 7.01306 ( 936) SS BOND : bond 0.00707 ( 21) SS BOND : angle 2.02579 ( 42) covalent geometry : bond 0.00366 (17040) covalent geometry : angle 0.81347 (23052) Misc. bond : bond 0.01285 ( 6) *********************** 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: 88 poor density : 220 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.6290 (ptt180) cc_final: 0.6024 (ptt90) REVERT: A 335 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5661 (p90) REVERT: A 449 LYS cc_start: 0.4842 (mptt) cc_final: 0.4579 (mptt) REVERT: A 475 MET cc_start: 0.4464 (mmt) cc_final: 0.3870 (mpp) REVERT: A 487 LYS cc_start: 0.3541 (OUTLIER) cc_final: 0.3266 (pmtt) REVERT: A 493 MET cc_start: -0.0301 (mtt) cc_final: -0.2627 (ttm) REVERT: B 37 LYS cc_start: 0.8338 (tttt) cc_final: 0.7966 (tmmt) REVERT: B 46 TRP cc_start: 0.1748 (t60) cc_final: 0.1458 (t60) REVERT: C 49 ARG cc_start: 0.6701 (ptp-170) cc_final: 0.6456 (ptp-170) REVERT: C 79 ILE cc_start: 0.3446 (OUTLIER) cc_final: 0.2991 (mp) REVERT: D 47 LYS cc_start: 0.6917 (ptpp) cc_final: 0.6519 (ptmm) REVERT: D 114 MET cc_start: 0.7467 (mmm) cc_final: 0.6907 (mtm) REVERT: D 452 LEU cc_start: 0.4166 (OUTLIER) cc_final: 0.3963 (tm) REVERT: E 3 LEU cc_start: 0.5026 (OUTLIER) cc_final: 0.4724 (pp) REVERT: E 80 MET cc_start: 0.4225 (tpt) cc_final: 0.3849 (tmm) REVERT: G 328 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6871 (tp) REVERT: G 447 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5122 (tmm160) REVERT: H 33 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5419 (tmm) REVERT: H 69 MET cc_start: 0.0892 (OUTLIER) cc_final: -0.0192 (pmm) outliers start: 88 outliers final: 34 residues processed: 285 average time/residue: 0.9906 time to fit residues: 323.7482 Evaluate side-chains 222 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 332 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 G residue 33 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain I residue 80 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 0.0030 chunk 137 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 167 optimal weight: 0.0980 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.175734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.134705 restraints weight = 25299.447| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 2.95 r_work: 0.4453 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.9174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17076 Z= 0.194 Angle : 0.867 14.476 23121 Z= 0.440 Chirality : 0.050 0.248 2511 Planarity : 0.006 0.065 3015 Dihedral : 9.719 174.989 2502 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.73 % Favored : 89.22 % Rotamer: Outliers : 5.81 % Allowed : 22.04 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 5.56 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.15), residues: 2106 helix: -1.70 (0.25), residues: 303 sheet: -2.94 (0.21), residues: 474 loop : -3.11 (0.14), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 340 HIS 0.008 0.002 HIS F 80 PHE 0.036 0.003 PHE G 93 TYR 0.022 0.002 TYR D 274 ARG 0.023 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 9) link_NAG-ASN : angle 3.15540 ( 27) hydrogen bonds : bond 0.05540 ( 363) hydrogen bonds : angle 6.91051 ( 936) SS BOND : bond 0.00520 ( 21) SS BOND : angle 2.16543 ( 42) covalent geometry : bond 0.00442 (17040) covalent geometry : angle 0.85645 (23052) Misc. bond : bond 0.01346 ( 6) *********************** 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 304 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 199 time to evaluate : 1.681 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 193 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6422 (tt) REVERT: A 475 MET cc_start: 0.4403 (mmt) cc_final: 0.3843 (mpp) REVERT: A 487 LYS cc_start: 0.3757 (OUTLIER) cc_final: 0.3425 (pmtt) REVERT: A 493 MET cc_start: -0.0245 (mtt) cc_final: -0.2597 (ttm) REVERT: B 37 LYS cc_start: 0.8386 (tttt) cc_final: 0.8008 (tmmt) REVERT: B 46 TRP cc_start: 0.1869 (t60) cc_final: 0.1535 (t60) REVERT: B 69 MET cc_start: 0.2056 (tpt) cc_final: 0.0912 (tpt) REVERT: C 37 MET cc_start: 0.6139 (tpt) cc_final: 0.5934 (tpt) REVERT: C 49 ARG cc_start: 0.6717 (ptp-170) cc_final: 0.6497 (ptp-170) REVERT: C 79 ILE cc_start: 0.3359 (OUTLIER) cc_final: 0.2898 (mp) REVERT: D 47 LYS cc_start: 0.6652 (ptpp) cc_final: 0.6309 (ptmm) REVERT: D 114 MET cc_start: 0.7491 (mmm) cc_final: 0.6815 (mtm) REVERT: D 452 LEU cc_start: 0.4462 (OUTLIER) cc_final: 0.4018 (tm) REVERT: E 3 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4836 (pp) REVERT: E 80 MET cc_start: 0.4617 (tpt) cc_final: 0.4251 (tmm) REVERT: G 36 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5928 (ptp-170) REVERT: G 103 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7094 (mm) REVERT: G 447 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5195 (tmm160) REVERT: H 33 MET cc_start: 0.6282 (ptt) cc_final: 0.5603 (tmm) REVERT: H 69 MET cc_start: 0.0940 (OUTLIER) cc_final: -0.0639 (pmm) outliers start: 105 outliers final: 46 residues processed: 274 average time/residue: 1.0785 time to fit residues: 341.4763 Evaluate side-chains 227 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 LEU 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 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 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 332 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 34 HIS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 212 ARG 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 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 80 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 131 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS G 388 GLN G 432 HIS ** 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 = 0.5162 r_free = 0.5162 target = 0.179335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.138274 restraints weight = 25054.866| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 2.91 r_work: 0.4480 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.9430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17076 Z= 0.174 Angle : 0.870 21.542 23121 Z= 0.436 Chirality : 0.050 0.239 2511 Planarity : 0.006 0.142 3015 Dihedral : 9.755 176.832 2502 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.82 % Allowed : 23.64 % Favored : 71.54 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.16), residues: 2106 helix: -1.51 (0.26), residues: 303 sheet: -2.80 (0.21), residues: 474 loop : -3.06 (0.14), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 340 HIS 0.008 0.001 HIS F 80 PHE 0.040 0.003 PHE A 137 TYR 0.022 0.002 TYR H 26 ARG 0.020 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 9) link_NAG-ASN : angle 6.01427 ( 27) hydrogen bonds : bond 0.05214 ( 363) hydrogen bonds : angle 6.80961 ( 936) SS BOND : bond 0.00602 ( 21) SS BOND : angle 2.30575 ( 42) covalent geometry : bond 0.00391 (17040) covalent geometry : angle 0.84100 (23052) Misc. bond : bond 0.01486 ( 6) *********************** 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 281 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 194 time to evaluate : 2.442 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 487 LYS cc_start: 0.3632 (OUTLIER) cc_final: 0.3420 (pmtt) REVERT: A 493 MET cc_start: -0.0487 (mtt) cc_final: -0.2693 (ttm) REVERT: B 37 LYS cc_start: 0.8344 (tttt) cc_final: 0.7935 (tmmt) REVERT: B 46 TRP cc_start: 0.1598 (t60) cc_final: 0.1363 (t60) REVERT: B 69 MET cc_start: 0.1404 (tpt) cc_final: 0.0442 (tpt) REVERT: C 79 ILE cc_start: 0.3353 (OUTLIER) cc_final: 0.2932 (mp) REVERT: D 114 MET cc_start: 0.7436 (mmm) cc_final: 0.6762 (mtm) REVERT: D 452 LEU cc_start: 0.4507 (OUTLIER) cc_final: 0.3975 (tm) REVERT: E 3 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4615 (pp) REVERT: E 80 MET cc_start: 0.4753 (tpt) cc_final: 0.4408 (tmm) REVERT: F 65 ARG cc_start: 0.2630 (OUTLIER) cc_final: 0.2159 (ppt170) REVERT: G 9 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5553 (p-80) REVERT: G 36 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5722 (ptp-170) REVERT: G 103 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7128 (mm) REVERT: G 388 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: G 447 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5168 (tmm160) REVERT: H 33 MET cc_start: 0.6408 (ptt) cc_final: 0.5747 (tmm) REVERT: H 69 MET cc_start: 0.0846 (OUTLIER) cc_final: -0.0642 (pmm) outliers start: 87 outliers final: 46 residues processed: 262 average time/residue: 1.3073 time to fit residues: 393.6845 Evaluate side-chains 226 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 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 34 HIS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 212 ARG 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 388 GLN Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain 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 H residue 106 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 7 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 197 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 38 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.179314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.138366 restraints weight = 24974.383| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 2.90 r_work: 0.4487 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.9696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17076 Z= 0.171 Angle : 0.843 13.525 23121 Z= 0.423 Chirality : 0.050 0.281 2511 Planarity : 0.005 0.091 3015 Dihedral : 9.921 176.993 2502 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.71 % Allowed : 24.64 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.16), residues: 2106 helix: -1.21 (0.28), residues: 288 sheet: -2.74 (0.22), residues: 474 loop : -3.01 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 409 HIS 0.009 0.001 HIS F 80 PHE 0.032 0.003 PHE A 93 TYR 0.023 0.002 TYR H 26 ARG 0.009 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 9) link_NAG-ASN : angle 2.85608 ( 27) hydrogen bonds : bond 0.05083 ( 363) hydrogen bonds : angle 6.76264 ( 936) SS BOND : bond 0.00542 ( 21) SS BOND : angle 2.20958 ( 42) covalent geometry : bond 0.00391 (17040) covalent geometry : angle 0.83305 (23052) Misc. bond : bond 0.01440 ( 6) *********************** 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 268 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 183 time to evaluate : 1.675 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 221 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.6111 (mmm160) REVERT: A 467 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.4789 (t80) REVERT: A 475 MET cc_start: 0.4197 (mmt) cc_final: 0.3796 (mpp) REVERT: A 493 MET cc_start: -0.1059 (mtt) cc_final: -0.3027 (ttm) REVERT: B 37 LYS cc_start: 0.8316 (tttt) cc_final: 0.7950 (tmmt) REVERT: B 46 TRP cc_start: 0.1618 (t60) cc_final: 0.1355 (t60) REVERT: C 79 ILE cc_start: 0.3370 (OUTLIER) cc_final: 0.2946 (mp) REVERT: D 9 HIS cc_start: 0.6636 (OUTLIER) cc_final: 0.5717 (p-80) REVERT: D 45 LYS cc_start: 0.6697 (tmmt) cc_final: 0.6358 (ttmt) REVERT: D 101 GLN cc_start: 0.5219 (OUTLIER) cc_final: 0.4668 (mt0) REVERT: D 114 MET cc_start: 0.7450 (mmm) cc_final: 0.6773 (mtm) REVERT: D 452 LEU cc_start: 0.4461 (OUTLIER) cc_final: 0.3893 (tm) REVERT: E 3 LEU cc_start: 0.4950 (OUTLIER) cc_final: 0.4488 (pp) REVERT: E 42 LYS cc_start: 0.7473 (mmmt) cc_final: 0.6950 (pmtt) REVERT: E 80 MET cc_start: 0.4996 (tpt) cc_final: 0.4671 (tmm) REVERT: F 49 ARG cc_start: 0.7182 (ptp-170) cc_final: 0.6925 (pmt170) REVERT: F 65 ARG cc_start: 0.2639 (OUTLIER) cc_final: 0.2263 (ppt170) REVERT: G 36 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6069 (ptt180) REVERT: G 103 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7103 (mm) REVERT: G 447 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5191 (tmm160) REVERT: H 33 MET cc_start: 0.6313 (ptt) cc_final: 0.5750 (tmm) REVERT: H 69 MET cc_start: 0.0344 (OUTLIER) cc_final: -0.0620 (pmm) outliers start: 85 outliers final: 49 residues processed: 250 average time/residue: 0.9969 time to fit residues: 288.5063 Evaluate side-chains 226 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 221 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 344 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 9 HIS 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 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 332 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 34 HIS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 464 PHE Chi-restraints excluded: chain 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 H residue 106 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 80 HIS Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 72 optimal weight: 7.9990 chunk 31 optimal weight: 0.0770 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 136 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 387 GLN A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 119 ASN E 34 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.182116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.141753 restraints weight = 25011.460| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 2.87 r_work: 0.4533 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.9886 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= 0.157 Angle : 0.845 18.582 23121 Z= 0.420 Chirality : 0.050 0.426 2511 Planarity : 0.005 0.080 3015 Dihedral : 9.274 178.415 2502 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.88 % Allowed : 25.80 % Favored : 70.32 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.16), residues: 2106 helix: -1.12 (0.29), residues: 297 sheet: -2.59 (0.23), residues: 462 loop : -2.93 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 409 HIS 0.009 0.001 HIS F 80 PHE 0.026 0.002 PHE A 93 TYR 0.020 0.002 TYR H 26 ARG 0.009 0.001 ARG G 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 9) link_NAG-ASN : angle 4.70014 ( 27) hydrogen bonds : bond 0.04827 ( 363) hydrogen bonds : angle 6.67323 ( 936) SS BOND : bond 0.00522 ( 21) SS BOND : angle 2.59390 ( 42) covalent geometry : bond 0.00357 (17040) covalent geometry : angle 0.82382 (23052) Misc. bond : bond 0.01273 ( 6) *********************** 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 258 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 188 time to evaluate : 1.714 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 221 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6179 (mtt180) REVERT: A 387 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: A 493 MET cc_start: -0.1232 (mtt) cc_final: -0.3087 (ttm) REVERT: B 37 LYS cc_start: 0.8277 (tttt) cc_final: 0.7906 (tmmt) REVERT: C 79 ILE cc_start: 0.3286 (OUTLIER) cc_final: 0.2841 (mp) REVERT: D 9 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.5893 (p-80) REVERT: D 45 LYS cc_start: 0.6740 (tmmt) cc_final: 0.6379 (ttmt) REVERT: D 114 MET cc_start: 0.7363 (mmm) cc_final: 0.6754 (mtm) REVERT: D 335 PHE cc_start: 0.6292 (p90) cc_final: 0.6086 (p90) REVERT: D 452 LEU cc_start: 0.4217 (OUTLIER) cc_final: 0.3800 (tm) REVERT: E 3 LEU cc_start: 0.4995 (OUTLIER) cc_final: 0.4445 (pp) REVERT: E 80 MET cc_start: 0.4889 (tpt) cc_final: 0.4637 (tmm) REVERT: F 49 ARG cc_start: 0.7131 (ptp-170) cc_final: 0.6918 (pmt170) REVERT: G 103 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7008 (mm) REVERT: G 447 ARG cc_start: 0.5773 (OUTLIER) cc_final: 0.5447 (ttt180) REVERT: H 33 MET cc_start: 0.6338 (ptt) cc_final: 0.5838 (tmm) REVERT: H 69 MET cc_start: 0.0245 (OUTLIER) cc_final: -0.0617 (pmm) REVERT: H 82 LEU cc_start: 0.5452 (mp) cc_final: 0.4600 (tp) outliers start: 70 outliers final: 39 residues processed: 242 average time/residue: 1.0430 time to fit residues: 288.3891 Evaluate side-chains 211 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 387 GLN 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 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 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 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 49 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 464 PHE 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 H residue 106 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 106 optimal weight: 0.0000 chunk 16 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 387 GLN A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.5105 r_free = 0.5105 target = 0.178094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.138246 restraints weight = 24886.709| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 3.03 r_work: 0.4494 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 1.0015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17076 Z= 0.172 Angle : 0.859 16.033 23121 Z= 0.428 Chirality : 0.050 0.290 2511 Planarity : 0.005 0.101 3015 Dihedral : 9.186 177.326 2502 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.27 % Allowed : 26.91 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.16), residues: 2106 helix: -1.19 (0.28), residues: 297 sheet: -2.51 (0.23), residues: 462 loop : -2.93 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 409 HIS 0.008 0.001 HIS F 80 PHE 0.029 0.003 PHE A 93 TYR 0.020 0.002 TYR H 26 ARG 0.009 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 3.87871 ( 27) hydrogen bonds : bond 0.04858 ( 363) hydrogen bonds : angle 6.63241 ( 936) SS BOND : bond 0.00556 ( 21) SS BOND : angle 2.61759 ( 42) covalent geometry : bond 0.00397 (17040) covalent geometry : angle 0.84229 (23052) Misc. bond : bond 0.01069 ( 6) ********************** 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 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LEU cc_start: 0.6338 (pt) cc_final: 0.5852 (tp) REVERT: B 37 LYS cc_start: 0.8285 (tttt) cc_final: 0.7923 (tmmt) REVERT: B 84 ARG cc_start: 0.3872 (pmt170) cc_final: 0.3572 (pmt170) REVERT: C 79 ILE cc_start: 0.3360 (OUTLIER) cc_final: 0.2958 (mp) REVERT: D 9 HIS cc_start: 0.6655 (OUTLIER) cc_final: 0.5755 (p-80) REVERT: D 45 LYS cc_start: 0.7118 (tmmt) cc_final: 0.6633 (ttmt) REVERT: D 114 MET cc_start: 0.7614 (mmm) cc_final: 0.7046 (mtm) REVERT: D 308 LEU cc_start: 0.6422 (pt) cc_final: 0.6091 (pp) REVERT: D 452 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3689 (tm) REVERT: E 3 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4558 (pp) REVERT: E 42 LYS cc_start: 0.7408 (mmmt) cc_final: 0.6969 (pmtt) REVERT: E 80 MET cc_start: 0.5066 (tpt) cc_final: 0.4800 (tmm) REVERT: F 49 ARG cc_start: 0.7152 (ptp-170) cc_final: 0.6941 (pmt170) REVERT: G 89 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6012 (m-80) REVERT: G 103 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7030 (mm) REVERT: G 308 LEU cc_start: 0.6376 (pt) cc_final: 0.5797 (tp) REVERT: G 447 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.5179 (tmm160) REVERT: H 33 MET cc_start: 0.6441 (ptt) cc_final: 0.5895 (tmm) REVERT: H 69 MET cc_start: 0.0229 (OUTLIER) cc_final: -0.0738 (pmm) outliers start: 59 outliers final: 43 residues processed: 216 average time/residue: 1.0103 time to fit residues: 249.7050 Evaluate side-chains 215 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 366 SER 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 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 156 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 414 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 49 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 464 PHE 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 H residue 106 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 0.0040 chunk 165 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 121 optimal weight: 0.0070 chunk 206 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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 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 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 HIS ** 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 = 0.5151 r_free = 0.5151 target = 0.182100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.141550 restraints weight = 24719.097| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 2.91 r_work: 0.4538 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 1.0239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17076 Z= 0.148 Angle : 0.816 16.821 23121 Z= 0.405 Chirality : 0.049 0.285 2511 Planarity : 0.005 0.065 3015 Dihedral : 8.903 178.891 2502 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.10 % Allowed : 27.30 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.16), residues: 2106 helix: -0.85 (0.29), residues: 282 sheet: -2.35 (0.23), residues: 489 loop : -2.84 (0.14), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 409 HIS 0.008 0.001 HIS F 80 PHE 0.021 0.002 PHE A 93 TYR 0.020 0.001 TYR H 26 ARG 0.008 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 9) link_NAG-ASN : angle 3.10753 ( 27) hydrogen bonds : bond 0.04567 ( 363) hydrogen bonds : angle 6.54531 ( 936) SS BOND : bond 0.00500 ( 21) SS BOND : angle 2.08553 ( 42) covalent geometry : bond 0.00335 (17040) covalent geometry : angle 0.80529 (23052) Misc. bond : bond 0.01106 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13867.26 seconds wall clock time: 240 minutes 58.78 seconds (14458.78 seconds total)