Starting phenix.real_space_refine on Sun May 18 07:12:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv0_35735/05_2025/8iv0_35735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv0_35735/05_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_35735/05_2025/8iv0_35735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv0_35735/05_2025/8iv0_35735.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv0_35735/05_2025/8iv0_35735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv0_35735/05_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-5687/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: 9.80, per 1000 atoms: 0.59 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: 4.16 Conformation dependent library (CDL) restraints added in 2.3 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: 2.23 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: 5.74 Time building geometry restraints manager: 4.89 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 38.860 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.010 ------------------------------------------------------------------------------- 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 : 1.708 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: 1.1526 time to fit residues: 498.2438 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 : 1.666 ------------------------------------------------------------------------------- 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 = 54)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.162139 restraints weight = 25114.252| |-----------------------------------------------------------------------------| 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 61.289 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 : 1.774 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: 0.4250 (mmt) cc_final: 0.3667 (mpp) REVERT: B 37 LYS cc_start: 0.8393 (tttt) cc_final: 0.7913 (tmmt) REVERT: B 42 LYS cc_start: 0.6093 (mttm) cc_final: 0.5839 (mmtp) REVERT: B 69 MET cc_start: 0.1669 (OUTLIER) cc_final: 0.0814 (tpt) REVERT: B 80 MET cc_start: 0.4570 (tpt) cc_final: 0.4191 (tpt) REVERT: D 449 LYS cc_start: 0.4175 (mmpt) cc_final: 0.2901 (tptt) REVERT: E 80 MET cc_start: 0.2845 (tpt) cc_final: 0.2481 (tmm) REVERT: G 156 MET cc_start: 0.4157 (mpt) cc_final: 0.3590 (mtt) REVERT: G 257 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.4289 (pmm) REVERT: G 475 MET cc_start: 0.2305 (mpt) cc_final: 0.1941 (mpt) outliers start: 80 outliers final: 24 residues processed: 339 average time/residue: 1.0628 time to fit residues: 407.3870 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 : 1.621 ------------------------------------------------------------------------------- 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: 0.8980 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 0.0470 chunk 97 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** 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** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.188293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.147746 restraints weight = 24973.535| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 2.97 r_work: 0.4629 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17076 Z= 0.196 Angle : 0.866 14.714 23121 Z= 0.442 Chirality : 0.051 0.238 2511 Planarity : 0.007 0.223 3015 Dihedral : 10.368 176.764 2502 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.93 % Favored : 90.98 % Rotamer: Outliers : 5.09 % Allowed : 18.05 % Favored : 76.85 % 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: -1.79 (0.26), residues: 288 sheet: -2.78 (0.21), residues: 465 loop : -3.37 (0.13), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 340 HIS 0.007 0.002 HIS F 80 PHE 0.027 0.003 PHE G 224 TYR 0.017 0.002 TYR D 364 ARG 0.028 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00747 ( 9) link_NAG-ASN : angle 3.43593 ( 27) hydrogen bonds : bond 0.06293 ( 363) hydrogen bonds : angle 7.02201 ( 936) SS BOND : bond 0.00442 ( 21) SS BOND : angle 2.17687 ( 42) covalent geometry : bond 0.00426 (17040) covalent geometry : angle 0.85396 (23052) Misc. bond : bond 0.01442 ( 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 322 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 230 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.4328 (mmt) cc_final: 0.3881 (mpp) REVERT: A 493 MET cc_start: -0.0079 (mtt) cc_final: -0.2529 (ttm) REVERT: B 37 LYS cc_start: 0.8351 (tttt) cc_final: 0.8022 (tmmt) REVERT: C 49 ARG cc_start: 0.6503 (ptp-170) cc_final: 0.6252 (pmt170) REVERT: C 74 ASP cc_start: 0.0864 (m-30) cc_final: 0.0656 (t0) REVERT: D 425 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6444 (pp) REVERT: D 452 LEU cc_start: 0.2878 (OUTLIER) cc_final: 0.2428 (tm) REVERT: E 3 LEU cc_start: 0.5019 (OUTLIER) cc_final: 0.4776 (pp) REVERT: E 69 MET cc_start: -0.0022 (tpt) cc_final: -0.1573 (pp-130) REVERT: E 80 MET cc_start: 0.3365 (tpt) cc_final: 0.2835 (tmm) REVERT: G 312 MET cc_start: 0.6765 (pmm) cc_final: 0.6562 (ptp) REVERT: G 465 GLU cc_start: 0.5244 (OUTLIER) cc_final: 0.4941 (tm-30) REVERT: G 493 MET cc_start: -0.1319 (mtt) cc_final: -0.1947 (mtt) REVERT: H 33 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.4402 (tmm) outliers start: 92 outliers final: 32 residues processed: 301 average time/residue: 0.9502 time to fit residues: 328.3604 Evaluate side-chains 219 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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 A residue 471 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 4 ILE 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 212 ARG Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 66 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 432 HIS A 481 ASN ** 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 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 HIS ** E 34 HIS ** 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 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 ASN G 431 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 = 0.5112 r_free = 0.5112 target = 0.177650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.135940 restraints weight = 25231.131| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 2.94 r_work: 0.4475 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.8319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 17076 Z= 0.225 Angle : 0.897 16.526 23121 Z= 0.459 Chirality : 0.052 0.247 2511 Planarity : 0.007 0.123 3015 Dihedral : 10.489 177.321 2502 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 5.65 % Allowed : 20.21 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 6.94 % 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: -4.30 (0.15), residues: 2106 helix: -1.63 (0.25), residues: 288 sheet: -2.84 (0.24), residues: 381 loop : -3.36 (0.13), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 409 HIS 0.009 0.002 HIS F 38 PHE 0.039 0.003 PHE D 464 TYR 0.025 0.003 TYR G 89 ARG 0.025 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 9) link_NAG-ASN : angle 3.05138 ( 27) hydrogen bonds : bond 0.06136 ( 363) hydrogen bonds : angle 7.04717 ( 936) SS BOND : bond 0.00574 ( 21) SS BOND : angle 2.17287 ( 42) covalent geometry : bond 0.00499 (17040) covalent geometry : angle 0.88726 (23052) Misc. bond : bond 0.01589 ( 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 337 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 235 time to evaluate : 1.608 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: 0.7108 (OUTLIER) cc_final: 0.6464 (tt) REVERT: A 335 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.5427 (p90) REVERT: A 487 LYS cc_start: 0.3568 (OUTLIER) cc_final: 0.3334 (pmtt) REVERT: A 493 MET cc_start: -0.0249 (mtt) cc_final: -0.2683 (ttm) REVERT: B 37 LYS cc_start: 0.8358 (tttt) cc_final: 0.7963 (tmmt) REVERT: B 46 TRP cc_start: 0.2381 (t60) cc_final: 0.1931 (t60) REVERT: B 49 VAL cc_start: 0.5243 (OUTLIER) cc_final: 0.5042 (p) REVERT: C 49 ARG cc_start: 0.6735 (ptp-170) cc_final: 0.6533 (ptp-170) REVERT: D 23 ARG cc_start: 0.6779 (mmm-85) cc_final: 0.5927 (tpp-160) REVERT: D 47 LYS cc_start: 0.7083 (ptpp) cc_final: 0.6880 (ptpp) REVERT: D 114 MET cc_start: 0.7450 (mmm) cc_final: 0.6848 (mtm) REVERT: E 80 MET cc_start: 0.4116 (tpt) cc_final: 0.3647 (tmm) REVERT: F 4 MET cc_start: 0.2638 (mmt) cc_final: 0.2260 (mmp) REVERT: G 447 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.3325 (ptt90) outliers start: 102 outliers final: 36 residues processed: 315 average time/residue: 1.0346 time to fit residues: 370.5849 Evaluate side-chains 221 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 215 VAL 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 467 PHE Chi-restraints excluded: chain A residue 471 ASP 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 49 VAL 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 13 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 110 ASP 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 263 VAL 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 I residue 10 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 10 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 202 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 GLN G 432 HIS H 34 HIS ** 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 = 0.5135 r_free = 0.5135 target = 0.179870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.139827 restraints weight = 25373.790| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 3.19 r_work: 0.4510 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.8760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 17076 Z= 0.177 Angle : 0.812 13.656 23121 Z= 0.412 Chirality : 0.050 0.327 2511 Planarity : 0.007 0.180 3015 Dihedral : 10.124 177.690 2502 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 5.04 % Allowed : 23.03 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % 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: -4.16 (0.15), residues: 2106 helix: -1.41 (0.27), residues: 285 sheet: -2.94 (0.22), residues: 450 loop : -3.18 (0.14), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 409 HIS 0.008 0.001 HIS D 8 PHE 0.032 0.003 PHE D 93 TYR 0.015 0.002 TYR D 274 ARG 0.024 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 9) link_NAG-ASN : angle 3.12379 ( 27) hydrogen bonds : bond 0.05388 ( 363) hydrogen bonds : angle 6.87066 ( 936) SS BOND : bond 0.00648 ( 21) SS BOND : angle 1.95483 ( 42) covalent geometry : bond 0.00404 (17040) covalent geometry : angle 0.80161 (23052) Misc. bond : bond 0.01579 ( 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 296 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 1.896 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 193 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6513 (tt) REVERT: A 335 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5612 (p90) REVERT: A 467 PHE cc_start: 0.5361 (OUTLIER) cc_final: 0.5004 (m-80) REVERT: A 475 MET cc_start: 0.4278 (mmt) cc_final: 0.3731 (mpp) REVERT: A 493 MET cc_start: -0.0309 (mtt) cc_final: -0.2719 (ttm) REVERT: B 37 LYS cc_start: 0.8324 (tttt) cc_final: 0.7972 (tmmt) REVERT: C 49 ARG cc_start: 0.6640 (ptp-170) cc_final: 0.6378 (pmt170) REVERT: C 79 ILE cc_start: 0.3458 (OUTLIER) cc_final: 0.2995 (mp) REVERT: D 101 GLN cc_start: 0.5591 (OUTLIER) cc_final: 0.5014 (mt0) REVERT: D 114 MET cc_start: 0.7487 (mmm) cc_final: 0.6906 (mtm) REVERT: D 436 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6513 (pt) REVERT: D 452 LEU cc_start: 0.4041 (OUTLIER) cc_final: 0.3733 (tm) REVERT: E 3 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4713 (pp) REVERT: E 80 MET cc_start: 0.4243 (tpt) cc_final: 0.3924 (tmm) REVERT: F 4 MET cc_start: 0.2620 (mmt) cc_final: 0.2034 (mmp) REVERT: F 65 ARG cc_start: 0.2562 (OUTLIER) cc_final: 0.2210 (ppt170) REVERT: G 102 ILE cc_start: 0.6599 (pt) cc_final: 0.6381 (pp) REVERT: G 221 ARG cc_start: 0.5724 (mmp80) cc_final: 0.5067 (mmm160) REVERT: G 358 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6917 (tt0) REVERT: G 447 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.3418 (ptt90) REVERT: H 33 MET cc_start: 0.6170 (ptt) cc_final: 0.5241 (tmm) REVERT: H 69 MET cc_start: 0.0646 (OUTLIER) cc_final: -0.0118 (pmm) REVERT: I 78 ASN cc_start: 0.4491 (p0) cc_final: 0.3930 (t0) outliers start: 91 outliers final: 41 residues processed: 268 average time/residue: 0.9734 time to fit residues: 300.4092 Evaluate side-chains 231 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 366 SER 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 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 49 THR Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR 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 272 ASP 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 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 I residue 10 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR 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: 0.9980 chunk 23 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 chunk 137 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 52 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.181872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.141472 restraints weight = 25125.241| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 3.35 r_work: 0.4493 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.9075 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= 0.168 Angle : 0.824 13.961 23121 Z= 0.418 Chirality : 0.049 0.276 2511 Planarity : 0.006 0.158 3015 Dihedral : 9.407 177.225 2502 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 4.65 % Allowed : 23.03 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % 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 (0.15), residues: 2106 helix: -1.44 (0.26), residues: 300 sheet: -2.82 (0.22), residues: 462 loop : -3.08 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 340 HIS 0.008 0.001 HIS F 80 PHE 0.026 0.002 PHE A 464 TYR 0.016 0.002 TYR G 445 ARG 0.053 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 9) link_NAG-ASN : angle 3.03571 ( 27) hydrogen bonds : bond 0.05320 ( 363) hydrogen bonds : angle 6.75234 ( 936) SS BOND : bond 0.00575 ( 21) SS BOND : angle 1.64889 ( 42) covalent geometry : bond 0.00371 (17040) covalent geometry : angle 0.81536 (23052) Misc. bond : bond 0.02015 ( 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 283 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 199 time to evaluate : 1.663 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 475 MET cc_start: 0.4128 (mmt) cc_final: 0.3706 (mpp) REVERT: A 493 MET cc_start: -0.0275 (mtt) cc_final: -0.2635 (ttm) REVERT: B 37 LYS cc_start: 0.8335 (tttt) cc_final: 0.7924 (tmmt) REVERT: C 49 ARG cc_start: 0.6681 (ptp-170) cc_final: 0.6442 (pmt170) REVERT: C 79 ILE cc_start: 0.3410 (OUTLIER) cc_final: 0.2983 (mp) REVERT: D 47 LYS cc_start: 0.6790 (ptpp) cc_final: 0.6504 (ptmm) REVERT: D 114 MET cc_start: 0.7457 (mmm) cc_final: 0.6814 (mtm) REVERT: D 436 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6519 (pt) REVERT: D 446 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6786 (mm-30) REVERT: D 452 LEU cc_start: 0.3884 (OUTLIER) cc_final: 0.3660 (tm) REVERT: E 3 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4674 (pp) REVERT: E 80 MET cc_start: 0.4262 (tpt) cc_final: 0.3932 (tmm) REVERT: F 4 MET cc_start: 0.3024 (mmt) cc_final: 0.2537 (mmp) REVERT: F 65 ARG cc_start: 0.2017 (OUTLIER) cc_final: 0.1637 (ppt170) REVERT: G 9 HIS cc_start: 0.6666 (OUTLIER) cc_final: 0.6011 (p-80) REVERT: G 221 ARG cc_start: 0.5717 (mmp80) cc_final: 0.5092 (mmm160) REVERT: G 447 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5022 (tmm160) REVERT: H 33 MET cc_start: 0.6110 (ptt) cc_final: 0.5218 (tmm) REVERT: H 69 MET cc_start: 0.0566 (OUTLIER) cc_final: -0.0366 (pmm) REVERT: I 78 ASN cc_start: 0.4674 (p0) cc_final: 0.4425 (t0) outliers start: 84 outliers final: 44 residues processed: 265 average time/residue: 0.9855 time to fit residues: 298.8759 Evaluate side-chains 222 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU 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 31 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 87 VAL 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 328 LEU 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 69 MET Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 386 ASN A 481 ASN ** 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 GLN ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.176697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.135073 restraints weight = 25122.892| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 2.94 r_work: 0.4504 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.9442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17076 Z= 0.222 Angle : 0.898 18.630 23121 Z= 0.454 Chirality : 0.052 0.299 2511 Planarity : 0.006 0.100 3015 Dihedral : 9.573 173.904 2502 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 5.76 % Allowed : 23.03 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % 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: -4.09 (0.15), residues: 2106 helix: -1.53 (0.26), residues: 300 sheet: -2.82 (0.22), residues: 468 loop : -3.12 (0.14), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 409 HIS 0.008 0.002 HIS F 80 PHE 0.033 0.003 PHE A 93 TYR 0.024 0.002 TYR G 89 ARG 0.023 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 9) link_NAG-ASN : angle 3.21553 ( 27) hydrogen bonds : bond 0.05953 ( 363) hydrogen bonds : angle 6.88777 ( 936) SS BOND : bond 0.00714 ( 21) SS BOND : angle 1.79586 ( 42) covalent geometry : bond 0.00506 (17040) covalent geometry : angle 0.88974 (23052) Misc. bond : bond 0.01429 ( 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 291 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 187 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6594 (mtp85) REVERT: A 193 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6578 (tt) REVERT: A 467 PHE cc_start: 0.5345 (OUTLIER) cc_final: 0.5103 (m-80) REVERT: A 475 MET cc_start: 0.4224 (mmt) cc_final: 0.3735 (mpp) REVERT: A 493 MET cc_start: -0.0477 (mtt) cc_final: -0.2688 (ttm) REVERT: B 37 LYS cc_start: 0.8390 (tttt) cc_final: 0.7976 (tmmt) REVERT: B 46 TRP cc_start: 0.2111 (t60) cc_final: 0.1838 (t60) REVERT: B 69 MET cc_start: 0.1758 (OUTLIER) cc_final: 0.0635 (tpt) REVERT: C 49 ARG cc_start: 0.6863 (ptp-170) cc_final: 0.6654 (ptp-170) REVERT: C 79 ILE cc_start: 0.3465 (OUTLIER) cc_final: 0.3014 (mp) REVERT: D 114 MET cc_start: 0.7559 (mmm) cc_final: 0.6893 (mtm) REVERT: E 3 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4773 (pp) REVERT: E 80 MET cc_start: 0.4889 (tpt) cc_final: 0.4552 (tmm) REVERT: F 4 MET cc_start: 0.2849 (mmt) cc_final: 0.2261 (mmp) REVERT: F 65 ARG cc_start: 0.2273 (OUTLIER) cc_final: 0.1792 (ppt170) REVERT: G 36 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.5426 (ptp-170) REVERT: G 447 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.5212 (tmm160) REVERT: H 33 MET cc_start: 0.6390 (ptt) cc_final: 0.5543 (tmm) REVERT: H 69 MET cc_start: 0.0499 (OUTLIER) cc_final: -0.0250 (pmm) outliers start: 104 outliers final: 54 residues processed: 265 average time/residue: 0.9116 time to fit residues: 278.6825 Evaluate side-chains 239 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 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 69 MET Chi-restraints excluded: chain B residue 83 ASP 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 31 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 328 LEU 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 69 MET Chi-restraints excluded: chain I residue 51 LEU 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: 0.5980 chunk 163 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 197 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5165 r_free = 0.5165 target = 0.180007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.138960 restraints weight = 24928.040| |-----------------------------------------------------------------------------| r_work (start): 0.4604 rms_B_bonded: 2.92 r_work: 0.4484 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.9646 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= 0.168 Angle : 0.842 16.835 23121 Z= 0.420 Chirality : 0.049 0.240 2511 Planarity : 0.006 0.085 3015 Dihedral : 9.349 177.477 2502 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.93 % Favored : 91.03 % Rotamer: Outliers : 4.54 % Allowed : 24.75 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.16), residues: 2106 helix: -1.43 (0.27), residues: 300 sheet: -2.79 (0.22), residues: 462 loop : -3.03 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 409 HIS 0.009 0.001 HIS F 80 PHE 0.028 0.003 PHE G 93 TYR 0.023 0.002 TYR H 26 ARG 0.018 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 9) link_NAG-ASN : angle 3.59575 ( 27) hydrogen bonds : bond 0.05247 ( 363) hydrogen bonds : angle 6.83394 ( 936) SS BOND : bond 0.00619 ( 21) SS BOND : angle 1.98876 ( 42) covalent geometry : bond 0.00385 (17040) covalent geometry : angle 0.82956 (23052) Misc. bond : bond 0.01291 ( 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 280 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 198 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.5410 (OUTLIER) cc_final: 0.5172 (m-80) REVERT: A 475 MET cc_start: 0.4144 (mmt) cc_final: 0.3774 (mpp) REVERT: A 493 MET cc_start: -0.0927 (mtt) cc_final: -0.2965 (ttm) REVERT: B 37 LYS cc_start: 0.8318 (tttt) cc_final: 0.7937 (tmmt) REVERT: C 79 ILE cc_start: 0.3352 (OUTLIER) cc_final: 0.2875 (mp) REVERT: D 47 LYS cc_start: 0.6890 (ptpp) cc_final: 0.6528 (ptmm) REVERT: D 101 GLN cc_start: 0.4554 (OUTLIER) cc_final: 0.4277 (mp10) REVERT: E 3 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4556 (pp) REVERT: E 42 LYS cc_start: 0.7514 (mmmt) cc_final: 0.6987 (pmtt) REVERT: E 80 MET cc_start: 0.4938 (tpt) cc_final: 0.4635 (tmm) REVERT: F 4 MET cc_start: 0.3638 (mmt) cc_final: 0.3323 (mmp) REVERT: F 65 ARG cc_start: 0.2281 (OUTLIER) cc_final: 0.1791 (ppt170) REVERT: G 9 HIS cc_start: 0.6514 (OUTLIER) cc_final: 0.5680 (p-80) REVERT: G 221 ARG cc_start: 0.5590 (mmp80) cc_final: 0.5076 (mmm160) REVERT: G 308 LEU cc_start: 0.6134 (pt) cc_final: 0.5492 (tp) REVERT: G 447 ARG cc_start: 0.5734 (OUTLIER) cc_final: 0.5119 (tmm160) REVERT: H 33 MET cc_start: 0.6308 (ptt) cc_final: 0.5694 (tmm) REVERT: H 69 MET cc_start: 0.0213 (OUTLIER) cc_final: -0.0463 (pmm) outliers start: 82 outliers final: 49 residues processed: 259 average time/residue: 0.9890 time to fit residues: 298.5661 Evaluate side-chains 228 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 171 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 234 THR 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 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 C residue 97 GLU 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 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 310 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 464 PHE 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 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 29 ASN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 276 SER 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 69 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 72 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.177903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.136791 restraints weight = 25128.285| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 2.92 r_work: 0.4460 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.9859 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= 0.189 Angle : 0.868 15.717 23121 Z= 0.436 Chirality : 0.051 0.273 2511 Planarity : 0.007 0.264 3015 Dihedral : 9.347 175.932 2502 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 4.26 % Allowed : 25.58 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 4.17 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.16), residues: 2106 helix: -1.47 (0.27), residues: 300 sheet: -2.79 (0.22), residues: 456 loop : -3.02 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 409 HIS 0.009 0.002 HIS F 80 PHE 0.030 0.003 PHE G 93 TYR 0.023 0.002 TYR H 26 ARG 0.040 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 9) link_NAG-ASN : angle 3.52767 ( 27) hydrogen bonds : bond 0.05326 ( 363) hydrogen bonds : angle 6.84117 ( 936) SS BOND : bond 0.00680 ( 21) SS BOND : angle 2.00881 ( 42) covalent geometry : bond 0.00434 (17040) covalent geometry : angle 0.85637 (23052) Misc. bond : bond 0.01576 ( 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 247 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.5527 (OUTLIER) cc_final: 0.5261 (m-80) REVERT: A 475 MET cc_start: 0.4171 (mmt) cc_final: 0.3804 (mpp) REVERT: A 493 MET cc_start: -0.0967 (mtt) cc_final: -0.2922 (ttm) REVERT: B 37 LYS cc_start: 0.8295 (tttt) cc_final: 0.7916 (tmmt) REVERT: C 49 ARG cc_start: 0.6670 (ptp-170) cc_final: 0.6425 (pmt170) REVERT: C 79 ILE cc_start: 0.3379 (OUTLIER) cc_final: 0.2948 (mp) REVERT: D 47 LYS cc_start: 0.7040 (ptpp) cc_final: 0.6688 (ptmm) REVERT: D 114 MET cc_start: 0.7568 (mmm) cc_final: 0.6907 (mtm) REVERT: D 452 LEU cc_start: 0.3774 (OUTLIER) cc_final: 0.3546 (tm) REVERT: E 3 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4519 (pp) REVERT: E 80 MET cc_start: 0.5147 (tpt) cc_final: 0.4814 (tmm) REVERT: F 4 MET cc_start: 0.3065 (mmt) cc_final: 0.2675 (mmp) REVERT: F 65 ARG cc_start: 0.2312 (OUTLIER) cc_final: 0.1924 (ppt170) REVERT: G 447 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5188 (tmm160) REVERT: H 33 MET cc_start: 0.6394 (ptt) cc_final: 0.5833 (tmm) REVERT: H 69 MET cc_start: 0.0348 (OUTLIER) cc_final: -0.0651 (pmm) outliers start: 77 outliers final: 54 residues processed: 228 average time/residue: 0.9600 time to fit residues: 251.5167 Evaluate side-chains 222 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 161 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 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 83 ASP 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 31 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 441 MET 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 F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 276 SER 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 69 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 157 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.176948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.137086 restraints weight = 25003.403| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 3.02 r_work: 0.4458 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.9979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17076 Z= 0.180 Angle : 0.861 17.637 23121 Z= 0.432 Chirality : 0.051 0.262 2511 Planarity : 0.005 0.059 3015 Dihedral : 9.223 177.079 2502 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.99 % Allowed : 26.14 % Favored : 69.88 % Cbeta Deviations : 0.05 % 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: -3.91 (0.16), residues: 2106 helix: -1.46 (0.27), residues: 300 sheet: -2.75 (0.23), residues: 456 loop : -2.96 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 409 HIS 0.009 0.001 HIS F 80 PHE 0.028 0.003 PHE G 93 TYR 0.021 0.002 TYR H 26 ARG 0.011 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 9) link_NAG-ASN : angle 3.29028 ( 27) hydrogen bonds : bond 0.05120 ( 363) hydrogen bonds : angle 6.84408 ( 936) SS BOND : bond 0.00649 ( 21) SS BOND : angle 1.83163 ( 42) covalent geometry : bond 0.00408 (17040) covalent geometry : angle 0.85085 (23052) Misc. bond : bond 0.01812 ( 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 250 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 1.711 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: 0.4111 (mmt) cc_final: 0.3910 (mpp) REVERT: A 493 MET cc_start: -0.0776 (mtt) cc_final: -0.2704 (ttm) REVERT: B 22 LYS cc_start: 0.5527 (pptt) cc_final: 0.4575 (pmtt) REVERT: B 37 LYS cc_start: 0.8277 (tttt) cc_final: 0.7885 (tmmt) REVERT: C 79 ILE cc_start: 0.3331 (OUTLIER) cc_final: 0.2844 (mp) REVERT: D 47 LYS cc_start: 0.6963 (ptpp) cc_final: 0.6615 (ptmm) REVERT: D 114 MET cc_start: 0.7670 (mmm) cc_final: 0.7112 (mtm) REVERT: E 3 LEU cc_start: 0.5124 (OUTLIER) cc_final: 0.4558 (pp) REVERT: E 42 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6967 (pmtt) REVERT: E 80 MET cc_start: 0.5252 (tpt) cc_final: 0.4968 (tmm) REVERT: F 4 MET cc_start: 0.3049 (mmt) cc_final: 0.2677 (mmp) REVERT: F 24 ARG cc_start: 0.5235 (mtp85) cc_final: 0.4951 (ttt90) REVERT: F 65 ARG cc_start: 0.2577 (OUTLIER) cc_final: 0.2121 (ppt170) REVERT: G 447 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5128 (tmm160) REVERT: H 33 MET cc_start: 0.6395 (ptt) cc_final: 0.5912 (tmm) REVERT: H 69 MET cc_start: 0.0027 (OUTLIER) cc_final: -0.0890 (pmm) outliers start: 72 outliers final: 55 residues processed: 230 average time/residue: 0.9196 time to fit residues: 244.3270 Evaluate side-chains 229 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 234 THR 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 B residue 3 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 83 ASP 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 15 THR 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 189 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 418 TRP Chi-restraints excluded: chain D residue 441 MET 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 F residue 31 THR Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 212 ARG Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 276 SER 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 69 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 121 optimal weight: 0.0170 chunk 206 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 430 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 314 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 = 0.178324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.138157 restraints weight = 24792.072| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 3.11 r_work: 0.4469 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 1.0159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17076 Z= 0.166 Angle : 0.846 17.374 23121 Z= 0.423 Chirality : 0.050 0.257 2511 Planarity : 0.005 0.061 3015 Dihedral : 9.115 178.102 2502 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.88 % Allowed : 26.52 % Favored : 69.60 % 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: -3.74 (0.16), residues: 2106 helix: -1.30 (0.28), residues: 294 sheet: -2.52 (0.23), residues: 483 loop : -2.89 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 409 HIS 0.009 0.001 HIS F 80 PHE 0.026 0.002 PHE G 93 TYR 0.021 0.002 TYR H 26 ARG 0.009 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 9) link_NAG-ASN : angle 3.14029 ( 27) hydrogen bonds : bond 0.04912 ( 363) hydrogen bonds : angle 6.75565 ( 936) SS BOND : bond 0.00650 ( 21) SS BOND : angle 1.64490 ( 42) covalent geometry : bond 0.00376 (17040) covalent geometry : angle 0.83776 (23052) Misc. bond : bond 0.01563 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12636.88 seconds wall clock time: 218 minutes 12.19 seconds (13092.19 seconds total)