Starting phenix.real_space_refine on Thu Aug 6 13:00:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n3b_48850/08_2026/9n3b_48850.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n3b_48850/08_2026/9n3b_48850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n3b_48850/08_2026/9n3b_48850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n3b_48850/08_2026/9n3b_48850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n3b_48850/08_2026/9n3b_48850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n3b_48850/08_2026/9n3b_48850.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.098 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 9421 2.51 5 N 2538 2.21 5 O 2803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14852 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3769 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 17, 'TRANS': 482} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 578 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3769 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 17, 'TRANS': 482} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 578 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "E" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3769 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 17, 'TRANS': 482} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 578 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 957 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.91, per 1000 atoms: 0.20 Number of scatterers: 14852 At special positions: 0 Unit cell: (128.02, 112.45, 186.84, 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 2803 8.00 N 2538 7.00 C 9421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.02 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 305 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 288 " distance=2.03 Simple disulfide: pdb=" SG CYS E 305 " - pdb=" SG CYS E 336 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 154 " " NAG C 601 " - " ASN C 154 " " NAG E 601 " - " ASN E 154 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 630.2 milliseconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3516 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 33 sheets defined 29.2% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.517A pdb=" N GLY A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.557A pdb=" N THR A 238 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 402 through 422 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 434 through 454 removed outlier: 4.215A pdb=" N GLN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 475 Processing helix chain 'A' and resid 478 through 498 Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.969A pdb=" N LEU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 75 removed outlier: 3.736A pdb=" N ALA B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.605A pdb=" N ARG C 85 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 192 through 195 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 215 through 221 removed outlier: 3.501A pdb=" N LEU C 221 " --> pdb=" O TRP C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 238 removed outlier: 3.734A pdb=" N THR C 238 " --> pdb=" O ASN C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 402 through 422 removed outlier: 3.882A pdb=" N ALA C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 449 through 455 removed outlier: 3.871A pdb=" N LEU C 453 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 475 removed outlier: 3.616A pdb=" N ASN C 475 " --> pdb=" O TRP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 498 Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.627A pdb=" N THR D 23 " --> pdb=" O MET D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 39 Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.866A pdb=" N ALA D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 74 removed outlier: 3.836A pdb=" N ALA D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'E' and resid 181 through 183 No H-bonds generated for 'chain 'E' and resid 181 through 183' Processing helix chain 'E' and resid 192 through 195 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 215 through 221 Processing helix chain 'E' and resid 235 through 238 removed outlier: 3.513A pdb=" N THR E 238 " --> pdb=" O ASN E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 235 through 238' Processing helix chain 'E' and resid 258 through 266 Processing helix chain 'E' and resid 388 through 392 removed outlier: 3.672A pdb=" N GLN E 391 " --> pdb=" O ARG E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 422 Processing helix chain 'E' and resid 423 through 428 Processing helix chain 'E' and resid 434 through 454 removed outlier: 3.931A pdb=" N ALA E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 475 removed outlier: 3.565A pdb=" N MET E 472 " --> pdb=" O LEU E 468 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN E 475 " --> pdb=" O TRP E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 499 removed outlier: 3.592A pdb=" N SER E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 29 through 39 removed outlier: 3.701A pdb=" N TRP F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 53 removed outlier: 3.873A pdb=" N LEU F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 75 removed outlier: 3.726A pdb=" N VAL F 62 " --> pdb=" O MET F 58 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.555A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.209A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU A 138 " --> pdb=" O MET A 46 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N MET A 48 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS A 136 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.209A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 26 removed outlier: 3.587A pdb=" N THR A 187 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 removed outlier: 6.014A pdb=" N GLU A 55 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR A 129 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG A 57 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 127 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 210 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 270 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA6, first strand: chain 'A' and resid 68 through 73 removed outlier: 3.823A pdb=" N GLY A 109 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 115 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA8, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA9, first strand: chain 'A' and resid 340 through 343 Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 12 removed outlier: 7.035A pdb=" N ASN C 8 " --> pdb=" O CYS C 30 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N THR C 32 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N SER C 29 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N MET C 45 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU C 138 " --> pdb=" O MET C 46 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N MET C 48 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS C 136 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.575A pdb=" N LEU C 23 " --> pdb=" O CYS C 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 99 removed outlier: 4.537A pdb=" N ILE C 113 " --> pdb=" O LYS C 71 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS C 71 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR C 115 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER C 69 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 117 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU C 67 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE C 119 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL C 65 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS C 121 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 63 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR C 123 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 57 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR C 129 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU C 55 " --> pdb=" O THR C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 99 removed outlier: 3.781A pdb=" N THR C 126 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE C 130 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N TYR C 201 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR C 210 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 240 through 242 Processing sheet with id=AB6, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AB7, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AB8, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AB9, first strand: chain 'C' and resid 340 through 343 removed outlier: 3.555A pdb=" N SER C 341 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 380 " --> pdb=" O LYS C 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.249A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU E 138 " --> pdb=" O MET E 46 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N MET E 48 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LYS E 136 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.249A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR E 210 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR E 201 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE E 130 " --> pdb=" O TYR E 201 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR E 126 " --> pdb=" O THR E 205 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 57 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR E 129 " --> pdb=" O GLU E 55 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU E 55 " --> pdb=" O THR E 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.667A pdb=" N LEU E 25 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 286 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 63 through 64 Processing sheet with id=AC5, first strand: chain 'E' and resid 68 through 73 removed outlier: 3.965A pdb=" N SER E 112 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 240 through 242 Processing sheet with id=AC7, first strand: chain 'E' and resid 309 through 310 Processing sheet with id=AC8, first strand: chain 'E' and resid 309 through 310 removed outlier: 3.724A pdb=" N ALA E 369 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 340 through 343 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AD2, first strand: chain 'H' and resid 18 through 22 removed outlier: 4.209A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.507A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 115 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD5, first strand: chain 'L' and resid 33 through 36 Processing sheet with id=AD6, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.890A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1725 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: 3.39 Time building geometry restraints manager: 1.44 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: 4573 1.33 - 1.45: 2458 1.45 - 1.57: 8005 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 15174 Sorted by residual: bond pdb=" CB GLU A 26 " pdb=" CG GLU A 26 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.69e+00 bond pdb=" CG GLU A 26 " pdb=" CD GLU A 26 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CB TRP E 397 " pdb=" CG TRP E 397 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.32e+00 bond pdb=" CG ARG L 90 " pdb=" CD ARG L 90 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB MET L 4 " pdb=" CG MET L 4 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 2.00e+00 ... (remaining 15169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20137 2.04 - 4.09: 403 4.09 - 6.13: 43 6.13 - 8.17: 4 8.17 - 10.21: 1 Bond angle restraints: 20588 Sorted by residual: angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 102.49 10.21 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N MET L 4 " pdb=" CA MET L 4 " pdb=" C MET L 4 " ideal model delta sigma weight residual 111.02 114.51 -3.49 1.25e+00 6.40e-01 7.78e+00 angle pdb=" N THR E 248 " pdb=" CA THR E 248 " pdb=" C THR E 248 " ideal model delta sigma weight residual 108.60 104.69 3.91 1.46e+00 4.69e-01 7.17e+00 angle pdb=" C ALA A 18 " pdb=" N THR A 19 " pdb=" CA THR A 19 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 angle pdb=" N GLU A 26 " pdb=" CA GLU A 26 " pdb=" C GLU A 26 " ideal model delta sigma weight residual 108.26 112.52 -4.26 1.66e+00 3.63e-01 6.58e+00 ... (remaining 20583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 8300 17.41 - 34.82: 510 34.82 - 52.24: 115 52.24 - 69.65: 16 69.65 - 87.06: 12 Dihedral angle restraints: 8953 sinusoidal: 3435 harmonic: 5518 Sorted by residual: dihedral pdb=" CA VAL H 124 " pdb=" C VAL H 124 " pdb=" N SER H 125 " pdb=" CA SER H 125 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ALA C 228 " pdb=" C ALA C 228 " pdb=" N GLU C 229 " pdb=" CA GLU C 229 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LEU A 12 " pdb=" C LEU A 12 " pdb=" N GLU A 13 " pdb=" CA GLU A 13 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 8950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1694 0.048 - 0.096: 550 0.096 - 0.144: 107 0.144 - 0.192: 3 0.192 - 0.240: 1 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CB ILE L 29 " pdb=" CA ILE L 29 " pdb=" CG1 ILE L 29 " pdb=" CG2 ILE L 29 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO A 171 " pdb=" N PRO A 171 " pdb=" C PRO A 171 " pdb=" CB PRO A 171 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA MET L 4 " pdb=" N MET L 4 " pdb=" C MET L 4 " pdb=" CB MET L 4 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 2352 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 124 " 0.031 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C VAL H 124 " -0.107 2.00e-02 2.50e+03 pdb=" O VAL H 124 " 0.041 2.00e-02 2.50e+03 pdb=" N SER H 125 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 99 " 0.205 9.50e-02 1.11e+02 9.25e-02 6.63e+00 pdb=" NE ARG E 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG E 99 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG E 99 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG E 99 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " -0.183 9.50e-02 1.11e+02 8.24e-02 5.09e+00 pdb=" NE ARG A 128 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " -0.001 2.00e-02 2.50e+03 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 8440 2.99 - 3.47: 15172 3.47 - 3.94: 23433 3.94 - 4.42: 26475 4.42 - 4.90: 42541 Nonbonded interactions: 116061 Sorted by model distance: nonbonded pdb=" O THR B 23 " pdb=" OG1 THR B 23 " model vdw 2.509 3.040 nonbonded pdb=" N ASP C 197 " pdb=" OD1 ASP C 197 " model vdw 2.513 3.120 nonbonded pdb=" O THR D 23 " pdb=" OG1 THR D 23 " model vdw 2.534 3.040 nonbonded pdb=" O ALA A 18 " pdb=" OG1 THR A 19 " model vdw 2.535 3.040 nonbonded pdb=" O THR E 332 " pdb=" OG1 THR E 332 " model vdw 2.535 3.040 ... (remaining 116056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.250 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.280 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.006 0.058 15194 Z= 0.287 Angle : 0.709 10.213 20631 Z= 0.382 Chirality : 0.046 0.240 2355 Planarity : 0.006 0.092 2606 Dihedral : 12.424 87.059 5386 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.20 % Allowed : 10.69 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.18), residues: 1942 helix: -0.18 (0.23), residues: 486 sheet: -0.52 (0.24), residues: 464 loop : -1.14 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG E 99 TYR 0.037 0.004 TYR A 202 PHE 0.023 0.002 PHE E 211 TRP 0.027 0.002 TRP E 459 HIS 0.007 0.002 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (15174) covalent geometry : angle 0.70683 / 0.38 (20588) SS BOND : bond 0.00378 / 0.20 ( 17) SS BOND : angle 1.06376 / 0.65 ( 34) hydrogen bonds : bond 0.21774 / 14.41 ( 621) hydrogen bonds : angle 8.61021 / 5.98 ( 1725) link_NAG-ASN : bond 0.00130 / 0.07 ( 3) link_NAG-ASN : angle 1.96251 / 1.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 656 time to evaluate : 0.394 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 34 MET cc_start: 0.8383 (ptp) cc_final: 0.8072 (ptp) REVERT: A 42 ASP cc_start: 0.7667 (m-30) cc_final: 0.7230 (m-30) REVERT: A 45 MET cc_start: 0.8780 (ppp) cc_final: 0.8525 (ppp) REVERT: A 46 MET cc_start: 0.8075 (mtp) cc_final: 0.6959 (mtt) REVERT: A 47 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8573 (p0) REVERT: A 87 ASP cc_start: 0.7781 (m-30) cc_final: 0.7401 (t0) REVERT: A 105 CYS cc_start: 0.8136 (m) cc_final: 0.7213 (m) REVERT: A 114 ASP cc_start: 0.7728 (t0) cc_final: 0.7261 (t0) REVERT: A 132 LYS cc_start: 0.8937 (mttt) cc_final: 0.8495 (mmtt) REVERT: A 135 ILE cc_start: 0.9269 (mm) cc_final: 0.9011 (mt) REVERT: A 138 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: A 185 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6755 (mm-30) REVERT: A 191 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 238 THR cc_start: 0.8586 (m) cc_final: 0.8175 (m) REVERT: A 239 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8902 (tp) REVERT: A 241 GLU cc_start: 0.2491 (tt0) cc_final: 0.1263 (mt-10) REVERT: A 253 ILE cc_start: 0.9474 (tp) cc_final: 0.9272 (tp) REVERT: A 273 GLU cc_start: 0.6218 (tp30) cc_final: 0.5977 (tp30) REVERT: A 322 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9313 (p) REVERT: A 376 GLU cc_start: 0.9081 (tp30) cc_final: 0.8659 (tp30) REVERT: A 382 SER cc_start: 0.8986 (p) cc_final: 0.8779 (m) REVERT: A 413 LYS cc_start: 0.9404 (tppp) cc_final: 0.9130 (tppp) REVERT: A 450 PHE cc_start: 0.9298 (t80) cc_final: 0.9028 (t80) REVERT: A 464 LEU cc_start: 0.9093 (mt) cc_final: 0.8274 (tt) REVERT: A 465 LEU cc_start: 0.9600 (tp) cc_final: 0.9311 (tp) REVERT: A 495 LEU cc_start: 0.9525 (mt) cc_final: 0.9220 (mt) REVERT: A 496 SER cc_start: 0.9260 (t) cc_final: 0.8823 (m) REVERT: B 21 ASP cc_start: 0.8356 (m-30) cc_final: 0.8131 (m-30) REVERT: B 28 TYR cc_start: 0.9323 (m-80) cc_final: 0.9040 (m-80) REVERT: B 42 TYR cc_start: 0.9173 (t80) cc_final: 0.8633 (t80) REVERT: B 53 LEU cc_start: 0.9314 (tt) cc_final: 0.9066 (tp) REVERT: B 56 ASN cc_start: 0.8686 (p0) cc_final: 0.8274 (p0) REVERT: B 58 MET cc_start: 0.8354 (tmm) cc_final: 0.7789 (tmm) REVERT: B 60 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8191 (mtp180) REVERT: C 6 MET cc_start: 0.8358 (mmm) cc_final: 0.8007 (mmm) REVERT: C 32 THR cc_start: 0.9520 (m) cc_final: 0.8751 (p) REVERT: C 46 MET cc_start: 0.7925 (mtt) cc_final: 0.7128 (mtt) REVERT: C 101 TRP cc_start: 0.9119 (m-10) cc_final: 0.8752 (m-10) REVERT: C 150 GLU cc_start: 0.8514 (pm20) cc_final: 0.8210 (pm20) REVERT: C 158 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8645 (mm-40) REVERT: C 180 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9067 (mm) REVERT: C 182 GLU cc_start: 0.8387 (pm20) cc_final: 0.7832 (pt0) REVERT: C 219 MET cc_start: 0.9171 (tpp) cc_final: 0.8903 (tpp) REVERT: C 229 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 234 ARG cc_start: 0.8516 (ptp90) cc_final: 0.8243 (mtm-85) REVERT: C 239 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7855 (mp) REVERT: C 264 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8848 (tm-30) REVERT: C 296 GLN cc_start: 0.8240 (pt0) cc_final: 0.7375 (pm20) REVERT: C 302 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.5408 (p90) REVERT: C 323 VAL cc_start: 0.9413 (t) cc_final: 0.9071 (m) REVERT: C 348 ASP cc_start: 0.8446 (t0) cc_final: 0.8244 (t70) REVERT: C 376 GLU cc_start: 0.8821 (tp30) cc_final: 0.8561 (tp30) REVERT: C 444 GLN cc_start: 0.8953 (tp40) cc_final: 0.8295 (tm-30) REVERT: C 457 MET cc_start: 0.8249 (ttt) cc_final: 0.8031 (ttm) REVERT: C 462 GLN cc_start: 0.9164 (mt0) cc_final: 0.8624 (mt0) REVERT: C 471 TRP cc_start: 0.8424 (t60) cc_final: 0.8100 (t60) REVERT: C 492 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9148 (mm) REVERT: D 35 TRP cc_start: 0.8951 (t60) cc_final: 0.8609 (t60) REVERT: D 63 PHE cc_start: 0.9129 (m-80) cc_final: 0.8871 (m-80) REVERT: D 74 TYR cc_start: 0.8219 (m-80) cc_final: 0.7901 (m-80) REVERT: E 19 THR cc_start: 0.9417 (p) cc_final: 0.9137 (p) REVERT: E 20 TRP cc_start: 0.8673 (t60) cc_final: 0.7853 (t60) REVERT: E 22 ASP cc_start: 0.7096 (t70) cc_final: 0.6631 (t70) REVERT: E 26 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7451 (mt-10) REVERT: E 38 LYS cc_start: 0.9360 (mmtp) cc_final: 0.8781 (mmtm) REVERT: E 45 MET cc_start: 0.8700 (tmm) cc_final: 0.7710 (tmm) REVERT: E 46 MET cc_start: 0.8440 (mtt) cc_final: 0.8153 (mtt) REVERT: E 87 ASP cc_start: 0.8979 (t0) cc_final: 0.8488 (t0) REVERT: E 96 VAL cc_start: 0.9551 (t) cc_final: 0.9228 (p) REVERT: E 133 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6188 (tt0) REVERT: E 169 ILE cc_start: 0.8722 (mm) cc_final: 0.8522 (tp) REVERT: E 280 LYS cc_start: 0.8780 (tttt) cc_final: 0.7530 (ttmt) REVERT: E 314 THR cc_start: 0.9027 (p) cc_final: 0.8373 (p) REVERT: E 374 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7558 (pp20) REVERT: E 383 TYR cc_start: 0.8729 (m-80) cc_final: 0.8075 (m-10) REVERT: E 391 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8212 (mm110) REVERT: E 421 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8785 (mm) REVERT: E 427 ASP cc_start: 0.8729 (m-30) cc_final: 0.7798 (m-30) REVERT: E 431 VAL cc_start: 0.9634 (OUTLIER) cc_final: 0.9177 (t) REVERT: E 451 ARG cc_start: 0.8890 (ptp-170) cc_final: 0.8257 (mmt180) REVERT: E 471 TRP cc_start: 0.8444 (t60) cc_final: 0.7781 (t60) REVERT: E 472 MET cc_start: 0.9235 (ptp) cc_final: 0.8405 (ppp) REVERT: E 477 ARG cc_start: 0.8827 (mmm160) cc_final: 0.8449 (ttp80) REVERT: E 478 ASP cc_start: 0.7620 (t0) cc_final: 0.7047 (t70) REVERT: F 24 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8759 (mtpt) REVERT: F 52 MET cc_start: 0.9007 (mmp) cc_final: 0.8803 (mmp) REVERT: F 53 LEU cc_start: 0.9481 (mt) cc_final: 0.9193 (mt) REVERT: F 56 ASN cc_start: 0.9202 (p0) cc_final: 0.8987 (p0) REVERT: F 63 PHE cc_start: 0.8637 (m-10) cc_final: 0.8237 (m-10) REVERT: H 13 GLN cc_start: 0.9394 (mp10) cc_final: 0.9050 (mm-40) REVERT: H 29 PHE cc_start: 0.7844 (p90) cc_final: 0.7247 (p90) REVERT: H 32 PHE cc_start: 0.8312 (m-80) cc_final: 0.7465 (m-80) REVERT: H 34 MET cc_start: 0.8258 (mpp) cc_final: 0.7892 (mmt) REVERT: H 39 GLN cc_start: 0.8599 (tp40) cc_final: 0.8396 (tp-100) REVERT: H 46 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7580 (tm-30) REVERT: H 47 TRP cc_start: 0.8858 (t60) cc_final: 0.7996 (t60) REVERT: H 67 ARG cc_start: 0.8198 (mtm110) cc_final: 0.6443 (mtm110) REVERT: H 80 CYS cc_start: 0.8595 (m) cc_final: 0.8136 (m) REVERT: H 82 GLN cc_start: 0.8613 (tp40) cc_final: 0.6879 (tm-30) REVERT: H 96 CYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6463 (m) REVERT: H 100 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7471 (ttm-80) REVERT: H 102 TYR cc_start: 0.8120 (p90) cc_final: 0.7708 (p90) REVERT: L 4 MET cc_start: 0.4883 (mmm) cc_final: 0.4586 (mmm) REVERT: L 48 ILE cc_start: 0.8849 (mp) cc_final: 0.8644 (mm) REVERT: L 79 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8185 (mm110) REVERT: L 83 PHE cc_start: 0.8192 (m-80) cc_final: 0.7685 (m-80) outliers start: 35 outliers final: 7 residues processed: 677 average time/residue: 0.0986 time to fit residues: 99.1605 Evaluate side-chains 548 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 530 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN B 7 HIS B 59 GLN C 2 ASN C 81 HIS D 5 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 328 GLN E 368 ASN ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 462 GLN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS L 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092651 restraints weight = 29568.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096042 restraints weight = 15088.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098399 restraints weight = 9595.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099998 restraints weight = 6950.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101085 restraints weight = 5531.935| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15194 Z= 0.269 Angle : 0.699 7.282 20631 Z= 0.373 Chirality : 0.045 0.175 2355 Planarity : 0.005 0.048 2606 Dihedral : 6.474 60.088 2172 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.35 % Allowed : 18.87 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1942 helix: 0.22 (0.23), residues: 492 sheet: -0.26 (0.24), residues: 496 loop : -1.00 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 215 TYR 0.030 0.003 TYR A 202 PHE 0.019 0.002 PHE C 119 TRP 0.019 0.002 TRP B 51 HIS 0.007 0.002 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 (15174) covalent geometry : angle 0.69779 / 0.37 (20588) SS BOND : bond 0.00336 / 0.17 ( 17) SS BOND : angle 1.02009 / 0.60 ( 34) hydrogen bonds : bond 0.04976 / 3.37 ( 621) hydrogen bonds : angle 6.23591 / 4.33 ( 1725) link_NAG-ASN : bond 0.00162 / 0.08 ( 3) link_NAG-ASN : angle 1.68398 / 1.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 574 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8537 (ptp) cc_final: 0.8250 (ptp) REVERT: A 42 ASP cc_start: 0.7811 (m-30) cc_final: 0.6942 (m-30) REVERT: A 46 MET cc_start: 0.8082 (mtp) cc_final: 0.7091 (mtt) REVERT: A 61 TYR cc_start: 0.8805 (p90) cc_final: 0.8588 (p90) REVERT: A 87 ASP cc_start: 0.7899 (m-30) cc_final: 0.7321 (t0) REVERT: A 105 CYS cc_start: 0.8013 (m) cc_final: 0.7184 (m) REVERT: A 114 ASP cc_start: 0.7837 (t0) cc_final: 0.7345 (t0) REVERT: A 132 LYS cc_start: 0.9200 (mttt) cc_final: 0.8275 (mmtt) REVERT: A 138 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: A 155 TYR cc_start: 0.9534 (t80) cc_final: 0.8965 (t80) REVERT: A 185 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6927 (mm-30) REVERT: A 191 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 196 ILE cc_start: 0.9297 (mp) cc_final: 0.9059 (mp) REVERT: A 240 MET cc_start: 0.8918 (mtm) cc_final: 0.8445 (mtm) REVERT: A 241 GLU cc_start: 0.3086 (tt0) cc_final: 0.1973 (mt-10) REVERT: A 376 GLU cc_start: 0.9201 (tp30) cc_final: 0.8601 (tp30) REVERT: A 413 LYS cc_start: 0.9284 (tppp) cc_final: 0.8864 (tppp) REVERT: A 457 MET cc_start: 0.8368 (mtp) cc_final: 0.7482 (ttm) REVERT: A 464 LEU cc_start: 0.9058 (mt) cc_final: 0.8211 (tt) REVERT: A 465 LEU cc_start: 0.9406 (tp) cc_final: 0.9140 (tp) REVERT: A 495 LEU cc_start: 0.9536 (mt) cc_final: 0.9219 (mt) REVERT: A 496 SER cc_start: 0.9234 (t) cc_final: 0.8677 (p) REVERT: B 21 ASP cc_start: 0.8365 (m-30) cc_final: 0.8003 (m-30) REVERT: B 33 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8505 (tt0) REVERT: B 42 TYR cc_start: 0.9041 (t80) cc_final: 0.8260 (t80) REVERT: B 53 LEU cc_start: 0.9187 (tt) cc_final: 0.8856 (tp) REVERT: B 56 ASN cc_start: 0.8819 (p0) cc_final: 0.8437 (p0) REVERT: B 58 MET cc_start: 0.8341 (tmm) cc_final: 0.7340 (tmm) REVERT: B 59 GLN cc_start: 0.8496 (pt0) cc_final: 0.7914 (pp30) REVERT: C 8 ASN cc_start: 0.8979 (m110) cc_final: 0.8664 (m110) REVERT: C 9 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8084 (ttm170) REVERT: C 45 MET cc_start: 0.8714 (tmm) cc_final: 0.8157 (tmm) REVERT: C 46 MET cc_start: 0.8195 (mtt) cc_final: 0.7868 (mtt) REVERT: C 61 TYR cc_start: 0.8280 (p90) cc_final: 0.7356 (p90) REVERT: C 101 TRP cc_start: 0.9100 (m-10) cc_final: 0.8723 (m-10) REVERT: C 180 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9051 (mm) REVERT: C 229 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7316 (tm-30) REVERT: C 264 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8772 (tm-30) REVERT: C 302 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.5679 (p90) REVERT: C 312 LEU cc_start: 0.9010 (mt) cc_final: 0.8517 (mt) REVERT: C 323 VAL cc_start: 0.9434 (t) cc_final: 0.9153 (m) REVERT: C 327 LEU cc_start: 0.8892 (tp) cc_final: 0.8651 (tp) REVERT: C 348 ASP cc_start: 0.8489 (t0) cc_final: 0.8219 (t70) REVERT: C 379 PHE cc_start: 0.8078 (m-80) cc_final: 0.7722 (m-10) REVERT: C 406 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8199 (tppt) REVERT: C 444 GLN cc_start: 0.8984 (tp40) cc_final: 0.8322 (tm-30) REVERT: C 457 MET cc_start: 0.8226 (ttt) cc_final: 0.7764 (ttt) REVERT: C 461 THR cc_start: 0.9290 (p) cc_final: 0.8846 (t) REVERT: C 471 TRP cc_start: 0.8408 (t60) cc_final: 0.8089 (t60) REVERT: D 35 TRP cc_start: 0.8964 (t60) cc_final: 0.8587 (t60) REVERT: D 74 TYR cc_start: 0.8116 (m-80) cc_final: 0.7747 (m-80) REVERT: E 22 ASP cc_start: 0.6669 (t70) cc_final: 0.6308 (t70) REVERT: E 26 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7546 (tt0) REVERT: E 38 LYS cc_start: 0.9347 (mmtp) cc_final: 0.8694 (mmtm) REVERT: E 45 MET cc_start: 0.8691 (tmm) cc_final: 0.7704 (tmm) REVERT: E 96 VAL cc_start: 0.9557 (t) cc_final: 0.9258 (p) REVERT: E 133 GLU cc_start: 0.5230 (mt-10) cc_final: 0.4805 (tt0) REVERT: E 178 LEU cc_start: 0.8632 (tp) cc_final: 0.8383 (tp) REVERT: E 182 GLU cc_start: 0.8704 (mp0) cc_final: 0.8286 (mp0) REVERT: E 209 LYS cc_start: 0.8127 (tppt) cc_final: 0.7776 (tppt) REVERT: E 220 ASP cc_start: 0.7887 (m-30) cc_final: 0.7558 (m-30) REVERT: E 221 LEU cc_start: 0.9273 (tp) cc_final: 0.8962 (tp) REVERT: E 273 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7150 (tm-30) REVERT: E 277 ASN cc_start: 0.8152 (t0) cc_final: 0.7908 (t0) REVERT: E 280 LYS cc_start: 0.8792 (tttt) cc_final: 0.8045 (ttmt) REVERT: E 294 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9367 (mmtm) REVERT: E 359 ASN cc_start: 0.9327 (p0) cc_final: 0.9068 (p0) REVERT: E 374 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7543 (pp20) REVERT: E 383 TYR cc_start: 0.8353 (m-80) cc_final: 0.7485 (m-10) REVERT: E 396 HIS cc_start: 0.8896 (t70) cc_final: 0.7915 (t70) REVERT: E 427 ASP cc_start: 0.8866 (m-30) cc_final: 0.8082 (m-30) REVERT: E 444 GLN cc_start: 0.8503 (mt0) cc_final: 0.7974 (tm-30) REVERT: E 451 ARG cc_start: 0.9006 (ptp-170) cc_final: 0.7913 (mmt180) REVERT: E 464 LEU cc_start: 0.9315 (tp) cc_final: 0.9059 (tp) REVERT: E 471 TRP cc_start: 0.8347 (t60) cc_final: 0.7678 (t60) REVERT: E 477 ARG cc_start: 0.8842 (mmm160) cc_final: 0.8444 (ttp80) REVERT: F 15 LYS cc_start: 0.9490 (mmmm) cc_final: 0.8297 (mmmm) REVERT: F 24 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8719 (mtpt) REVERT: F 59 GLN cc_start: 0.9076 (mt0) cc_final: 0.8649 (mp10) REVERT: F 69 LEU cc_start: 0.9258 (mt) cc_final: 0.8952 (mt) REVERT: H 12 VAL cc_start: 0.8876 (m) cc_final: 0.8656 (p) REVERT: H 13 GLN cc_start: 0.8843 (mp10) cc_final: 0.8538 (mm-40) REVERT: H 20 LEU cc_start: 0.8959 (mp) cc_final: 0.8662 (mt) REVERT: H 27 PHE cc_start: 0.7949 (p90) cc_final: 0.7468 (p90) REVERT: H 29 PHE cc_start: 0.7234 (p90) cc_final: 0.6632 (p90) REVERT: H 32 PHE cc_start: 0.8398 (m-80) cc_final: 0.7649 (m-80) REVERT: H 34 MET cc_start: 0.7591 (mpp) cc_final: 0.6912 (mmt) REVERT: H 45 LEU cc_start: 0.8493 (mt) cc_final: 0.7896 (mm) REVERT: H 46 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7559 (tm-30) REVERT: H 47 TRP cc_start: 0.8970 (t60) cc_final: 0.8080 (t60) REVERT: H 80 CYS cc_start: 0.8299 (m) cc_final: 0.7586 (m) REVERT: H 82 GLN cc_start: 0.7831 (tp40) cc_final: 0.7266 (tm-30) REVERT: H 96 CYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6606 (m) REVERT: L 24 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7810 (ttm110) REVERT: L 79 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7951 (mm110) REVERT: L 83 PHE cc_start: 0.8203 (m-80) cc_final: 0.7717 (m-80) REVERT: L 89 GLN cc_start: 0.7104 (tm130) cc_final: 0.6725 (tm-30) REVERT: L 98 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.7973 (m-80) outliers start: 85 outliers final: 54 residues processed: 608 average time/residue: 0.0983 time to fit residues: 90.1049 Evaluate side-chains 600 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 541 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 188 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN B 5 GLN B 7 HIS C 2 ASN E 258 GLN ** E 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 GLN E 396 HIS E 462 GLN ** F 7 HIS ** 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 = 0.3595 r_free = 0.3595 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096336 restraints weight = 29701.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099920 restraints weight = 14847.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102334 restraints weight = 9298.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103972 restraints weight = 6685.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105107 restraints weight = 5289.402| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15194 Z= 0.127 Angle : 0.609 9.199 20631 Z= 0.315 Chirality : 0.043 0.196 2355 Planarity : 0.004 0.040 2606 Dihedral : 5.719 66.286 2160 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.97 % Allowed : 21.38 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1942 helix: 0.42 (0.24), residues: 489 sheet: -0.13 (0.24), residues: 497 loop : -0.84 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 215 TYR 0.026 0.002 TYR E 201 PHE 0.024 0.001 PHE C 450 TRP 0.024 0.001 TRP B 51 HIS 0.007 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (15174) covalent geometry : angle 0.60805 / 0.31 (20588) SS BOND : bond 0.00254 / 0.14 ( 17) SS BOND : angle 0.89833 / 0.54 ( 34) hydrogen bonds : bond 0.04054 / 2.76 ( 621) hydrogen bonds : angle 5.51891 / 3.82 ( 1725) link_NAG-ASN : bond 0.00333 / 0.17 ( 3) link_NAG-ASN : angle 1.29149 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 601 time to evaluate : 0.422 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 34 MET cc_start: 0.8412 (ptp) cc_final: 0.8099 (ptp) REVERT: A 42 ASP cc_start: 0.7562 (m-30) cc_final: 0.6576 (m-30) REVERT: A 61 TYR cc_start: 0.8753 (p90) cc_final: 0.8526 (p90) REVERT: A 81 HIS cc_start: 0.7289 (t70) cc_final: 0.6910 (t70) REVERT: A 87 ASP cc_start: 0.7747 (m-30) cc_final: 0.7388 (t0) REVERT: A 105 CYS cc_start: 0.7929 (m) cc_final: 0.7037 (m) REVERT: A 114 ASP cc_start: 0.7788 (t0) cc_final: 0.7095 (t0) REVERT: A 132 LYS cc_start: 0.9002 (mttt) cc_final: 0.8187 (mmtt) REVERT: A 155 TYR cc_start: 0.9451 (t80) cc_final: 0.8933 (t80) REVERT: A 185 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6869 (mm-30) REVERT: A 191 GLU cc_start: 0.8749 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 240 MET cc_start: 0.8943 (mtm) cc_final: 0.8397 (mtm) REVERT: A 241 GLU cc_start: 0.1250 (tt0) cc_final: 0.0250 (mt-10) REVERT: A 283 SER cc_start: 0.8531 (m) cc_final: 0.7324 (t) REVERT: A 326 GLU cc_start: 0.7747 (mp0) cc_final: 0.7422 (mp0) REVERT: A 376 GLU cc_start: 0.9218 (tp30) cc_final: 0.8606 (tp30) REVERT: A 413 LYS cc_start: 0.9249 (tppp) cc_final: 0.8770 (tppp) REVERT: A 464 LEU cc_start: 0.8975 (mt) cc_final: 0.8097 (tt) REVERT: A 496 SER cc_start: 0.9253 (t) cc_final: 0.9029 (p) REVERT: B 21 ASP cc_start: 0.8352 (m-30) cc_final: 0.7929 (m-30) REVERT: B 28 TYR cc_start: 0.9447 (m-80) cc_final: 0.9184 (m-10) REVERT: B 42 TYR cc_start: 0.8905 (t80) cc_final: 0.8500 (t80) REVERT: B 53 LEU cc_start: 0.9143 (tt) cc_final: 0.8926 (tp) REVERT: B 56 ASN cc_start: 0.8642 (p0) cc_final: 0.8264 (p0) REVERT: B 58 MET cc_start: 0.8410 (tmm) cc_final: 0.7616 (tmm) REVERT: B 59 GLN cc_start: 0.8428 (pt0) cc_final: 0.7819 (pp30) REVERT: B 60 ARG cc_start: 0.8961 (ttm170) cc_final: 0.8422 (ttp-110) REVERT: C 8 ASN cc_start: 0.8893 (m110) cc_final: 0.8608 (m110) REVERT: C 9 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.7988 (ptm160) REVERT: C 45 MET cc_start: 0.8491 (tmm) cc_final: 0.7506 (tmm) REVERT: C 46 MET cc_start: 0.8083 (mtt) cc_final: 0.7779 (mtt) REVERT: C 55 GLU cc_start: 0.8340 (pm20) cc_final: 0.7382 (mp0) REVERT: C 61 TYR cc_start: 0.8014 (p90) cc_final: 0.7139 (p90) REVERT: C 77 MET cc_start: 0.7176 (ppp) cc_final: 0.6938 (ppp) REVERT: C 240 MET cc_start: 0.8349 (mmp) cc_final: 0.7999 (mmm) REVERT: C 264 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8961 (tm-30) REVERT: C 283 SER cc_start: 0.9242 (m) cc_final: 0.8906 (p) REVERT: C 292 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8025 (ptp) REVERT: C 302 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.4997 (p90) REVERT: C 323 VAL cc_start: 0.9419 (t) cc_final: 0.9163 (m) REVERT: C 327 LEU cc_start: 0.8834 (tp) cc_final: 0.8555 (tp) REVERT: C 348 ASP cc_start: 0.8276 (t0) cc_final: 0.8050 (t70) REVERT: C 373 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7822 (mp) REVERT: C 379 PHE cc_start: 0.7998 (m-80) cc_final: 0.7752 (m-10) REVERT: C 406 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8253 (tppt) REVERT: C 444 GLN cc_start: 0.8984 (tp40) cc_final: 0.8374 (tm-30) REVERT: C 457 MET cc_start: 0.7885 (ttt) cc_final: 0.7537 (ttt) REVERT: C 461 THR cc_start: 0.9307 (p) cc_final: 0.8894 (t) REVERT: C 471 TRP cc_start: 0.8369 (t60) cc_final: 0.7535 (t-100) REVERT: D 52 MET cc_start: 0.8896 (tpt) cc_final: 0.8661 (tpp) REVERT: D 74 TYR cc_start: 0.8208 (m-80) cc_final: 0.7745 (m-80) REVERT: E 22 ASP cc_start: 0.6786 (t70) cc_final: 0.6193 (t70) REVERT: E 26 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7053 (tt0) REVERT: E 38 LYS cc_start: 0.9249 (mmtp) cc_final: 0.8629 (mmtm) REVERT: E 45 MET cc_start: 0.8218 (tmm) cc_final: 0.7585 (tmm) REVERT: E 87 ASP cc_start: 0.8928 (t0) cc_final: 0.8281 (t0) REVERT: E 114 ASP cc_start: 0.7375 (m-30) cc_final: 0.7095 (m-30) REVERT: E 133 GLU cc_start: 0.6012 (mt-10) cc_final: 0.5630 (tt0) REVERT: E 149 VAL cc_start: 0.9236 (p) cc_final: 0.9011 (m) REVERT: E 182 GLU cc_start: 0.8655 (mp0) cc_final: 0.8304 (mp0) REVERT: E 191 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8217 (mm-30) REVERT: E 221 LEU cc_start: 0.9249 (tp) cc_final: 0.9034 (tp) REVERT: E 374 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: E 383 TYR cc_start: 0.8267 (m-80) cc_final: 0.7188 (m-10) REVERT: E 396 HIS cc_start: 0.8516 (t-90) cc_final: 0.7848 (t70) REVERT: E 397 TRP cc_start: 0.8983 (t-100) cc_final: 0.8504 (t-100) REVERT: E 427 ASP cc_start: 0.8849 (m-30) cc_final: 0.8029 (m-30) REVERT: E 451 ARG cc_start: 0.9188 (ptp-170) cc_final: 0.8081 (mmt180) REVERT: E 464 LEU cc_start: 0.9282 (tp) cc_final: 0.9025 (tp) REVERT: E 471 TRP cc_start: 0.8300 (t60) cc_final: 0.7698 (t-100) REVERT: E 477 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8455 (ttp80) REVERT: E 478 ASP cc_start: 0.7808 (t0) cc_final: 0.7269 (t70) REVERT: F 6 THR cc_start: 0.8682 (p) cc_final: 0.8462 (p) REVERT: F 15 LYS cc_start: 0.9605 (mmmm) cc_final: 0.8646 (mmmm) REVERT: F 20 MET cc_start: 0.7776 (mmm) cc_final: 0.7171 (mmm) REVERT: F 59 GLN cc_start: 0.9041 (mt0) cc_final: 0.8717 (mp10) REVERT: F 69 LEU cc_start: 0.9269 (mt) cc_final: 0.8913 (mt) REVERT: F 74 TYR cc_start: 0.8680 (m-80) cc_final: 0.8475 (m-80) REVERT: H 12 VAL cc_start: 0.8977 (m) cc_final: 0.8651 (p) REVERT: H 13 GLN cc_start: 0.8907 (mp10) cc_final: 0.8593 (mm-40) REVERT: H 29 PHE cc_start: 0.7107 (p90) cc_final: 0.6485 (p90) REVERT: H 32 PHE cc_start: 0.8147 (m-80) cc_final: 0.7639 (m-80) REVERT: H 34 MET cc_start: 0.7577 (mpp) cc_final: 0.6993 (mmt) REVERT: H 45 LEU cc_start: 0.8567 (mt) cc_final: 0.8282 (mt) REVERT: H 46 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7422 (tm-30) REVERT: H 47 TRP cc_start: 0.8970 (t60) cc_final: 0.8061 (t60) REVERT: H 67 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6632 (mtp85) REVERT: H 80 CYS cc_start: 0.8343 (m) cc_final: 0.7527 (m) REVERT: H 82 GLN cc_start: 0.7447 (tp40) cc_final: 0.6861 (tm-30) REVERT: H 90 ASP cc_start: 0.8650 (m-30) cc_final: 0.7841 (m-30) REVERT: H 96 CYS cc_start: 0.6911 (OUTLIER) cc_final: 0.5746 (m) REVERT: H 100 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7211 (ttm-80) REVERT: H 102 TYR cc_start: 0.8549 (p90) cc_final: 0.8179 (p90) REVERT: L 24 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7747 (ttm110) REVERT: L 28 ASN cc_start: 0.9046 (t0) cc_final: 0.8735 (m-40) REVERT: L 39 LYS cc_start: 0.7949 (mmmm) cc_final: 0.7608 (mmmm) REVERT: L 62 PHE cc_start: 0.7733 (m-80) cc_final: 0.6585 (m-80) REVERT: L 79 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7932 (mm110) REVERT: L 83 PHE cc_start: 0.8306 (m-80) cc_final: 0.7740 (m-80) REVERT: L 89 GLN cc_start: 0.6979 (tm130) cc_final: 0.6184 (tm-30) REVERT: L 90 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.5796 (ptm160) REVERT: L 92 PHE cc_start: 0.9189 (t80) cc_final: 0.8782 (t80) outliers start: 79 outliers final: 44 residues processed: 631 average time/residue: 0.0973 time to fit residues: 92.1551 Evaluate side-chains 597 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 546 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 77 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 59 optimal weight: 0.0570 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** F 7 HIS ** 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 = 0.3601 r_free = 0.3601 target = 0.123844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096638 restraints weight = 29698.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100238 restraints weight = 14770.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102656 restraints weight = 9220.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104317 restraints weight = 6623.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105434 restraints weight = 5230.160| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15194 Z= 0.143 Angle : 0.601 9.705 20631 Z= 0.309 Chirality : 0.043 0.201 2355 Planarity : 0.004 0.039 2606 Dihedral : 5.070 54.943 2151 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.35 % Allowed : 23.14 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1942 helix: 0.52 (0.24), residues: 462 sheet: -0.06 (0.25), residues: 485 loop : -0.78 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.021 0.002 TYR D 42 PHE 0.025 0.001 PHE C 450 TRP 0.015 0.001 TRP D 35 HIS 0.007 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (15174) covalent geometry : angle 0.59957 / 0.31 (20588) SS BOND : bond 0.00246 / 0.12 ( 17) SS BOND : angle 0.86681 / 0.53 ( 34) hydrogen bonds : bond 0.03718 / 2.55 ( 621) hydrogen bonds : angle 5.23261 / 3.62 ( 1725) link_NAG-ASN : bond 0.00173 / 0.09 ( 3) link_NAG-ASN : angle 1.32360 / 0.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 574 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7790 (m-30) cc_final: 0.6787 (m-30) REVERT: A 46 MET cc_start: 0.8793 (mmm) cc_final: 0.8514 (mmm) REVERT: A 48 MET cc_start: 0.9137 (ttp) cc_final: 0.8530 (ttp) REVERT: A 81 HIS cc_start: 0.7410 (t70) cc_final: 0.6936 (t70) REVERT: A 87 ASP cc_start: 0.7757 (m-30) cc_final: 0.7363 (t0) REVERT: A 105 CYS cc_start: 0.8091 (m) cc_final: 0.7172 (m) REVERT: A 132 LYS cc_start: 0.8938 (mttt) cc_final: 0.8170 (mmtt) REVERT: A 155 TYR cc_start: 0.9451 (t80) cc_final: 0.8974 (t80) REVERT: A 178 LEU cc_start: 0.9116 (tp) cc_final: 0.7908 (tt) REVERT: A 185 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 191 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 209 LYS cc_start: 0.8143 (tptt) cc_final: 0.7942 (ttmm) REVERT: A 240 MET cc_start: 0.8956 (mtm) cc_final: 0.8420 (mtm) REVERT: A 241 GLU cc_start: 0.1363 (tt0) cc_final: 0.0270 (mt-10) REVERT: A 283 SER cc_start: 0.8626 (m) cc_final: 0.7346 (t) REVERT: A 326 GLU cc_start: 0.7821 (mp0) cc_final: 0.7548 (mp0) REVERT: A 376 GLU cc_start: 0.9192 (tp30) cc_final: 0.8617 (tp30) REVERT: A 413 LYS cc_start: 0.9245 (tppp) cc_final: 0.8727 (tppp) REVERT: A 464 LEU cc_start: 0.8989 (mt) cc_final: 0.8097 (tt) REVERT: A 496 SER cc_start: 0.9273 (t) cc_final: 0.9058 (p) REVERT: B 42 TYR cc_start: 0.9005 (t80) cc_final: 0.8594 (t80) REVERT: B 56 ASN cc_start: 0.8614 (p0) cc_final: 0.8250 (p0) REVERT: B 58 MET cc_start: 0.8418 (tmm) cc_final: 0.7604 (tmm) REVERT: B 59 GLN cc_start: 0.8458 (pt0) cc_final: 0.7823 (pp30) REVERT: B 60 ARG cc_start: 0.9133 (ttm170) cc_final: 0.8812 (ttp-110) REVERT: C 8 ASN cc_start: 0.8890 (m110) cc_final: 0.8627 (m110) REVERT: C 9 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.7927 (ptm160) REVERT: C 45 MET cc_start: 0.8590 (tmm) cc_final: 0.7550 (tmm) REVERT: C 46 MET cc_start: 0.8049 (mtt) cc_final: 0.7845 (mtt) REVERT: C 55 GLU cc_start: 0.8364 (pm20) cc_final: 0.7405 (mp0) REVERT: C 61 TYR cc_start: 0.7861 (p90) cc_final: 0.7002 (p90) REVERT: C 84 LYS cc_start: 0.8918 (tppt) cc_final: 0.8717 (tppt) REVERT: C 107 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7586 (tt) REVERT: C 240 MET cc_start: 0.8447 (mmp) cc_final: 0.8193 (mmm) REVERT: C 259 GLU cc_start: 0.8997 (tt0) cc_final: 0.8776 (tt0) REVERT: C 264 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8972 (tm-30) REVERT: C 283 SER cc_start: 0.9074 (m) cc_final: 0.8666 (p) REVERT: C 302 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.4954 (p90) REVERT: C 346 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7881 (pp) REVERT: C 348 ASP cc_start: 0.8264 (t0) cc_final: 0.8036 (t70) REVERT: C 373 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7871 (mp) REVERT: C 376 GLU cc_start: 0.8865 (tp30) cc_final: 0.8653 (tp30) REVERT: C 379 PHE cc_start: 0.8122 (m-80) cc_final: 0.7865 (m-10) REVERT: C 406 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8268 (tppt) REVERT: C 444 GLN cc_start: 0.9005 (tp40) cc_final: 0.8351 (tm-30) REVERT: C 457 MET cc_start: 0.7990 (ttt) cc_final: 0.7643 (ttt) REVERT: C 461 THR cc_start: 0.9283 (p) cc_final: 0.8869 (t) REVERT: C 471 TRP cc_start: 0.8389 (t60) cc_final: 0.7529 (t-100) REVERT: D 35 TRP cc_start: 0.8910 (t60) cc_final: 0.8268 (t60) REVERT: D 52 MET cc_start: 0.8792 (tpt) cc_final: 0.8587 (tpp) REVERT: D 63 PHE cc_start: 0.9321 (m-80) cc_final: 0.9082 (m-80) REVERT: D 74 TYR cc_start: 0.8179 (m-80) cc_final: 0.7812 (m-80) REVERT: E 22 ASP cc_start: 0.6728 (t70) cc_final: 0.6135 (t70) REVERT: E 38 LYS cc_start: 0.9181 (mmtp) cc_final: 0.8546 (mmtm) REVERT: E 45 MET cc_start: 0.8177 (tmm) cc_final: 0.7462 (tmm) REVERT: E 133 GLU cc_start: 0.5075 (mt-10) cc_final: 0.4677 (tt0) REVERT: E 149 VAL cc_start: 0.9225 (p) cc_final: 0.9007 (m) REVERT: E 182 GLU cc_start: 0.8659 (mp0) cc_final: 0.8292 (mp0) REVERT: E 191 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8365 (mm-30) REVERT: E 209 LYS cc_start: 0.8184 (tppt) cc_final: 0.7691 (tptt) REVERT: E 220 ASP cc_start: 0.7773 (m-30) cc_final: 0.7360 (m-30) REVERT: E 221 LEU cc_start: 0.9258 (tp) cc_final: 0.9040 (tp) REVERT: E 273 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7291 (tm-30) REVERT: E 280 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: E 374 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: E 383 TYR cc_start: 0.8302 (m-80) cc_final: 0.7241 (m-80) REVERT: E 396 HIS cc_start: 0.8716 (t-90) cc_final: 0.8502 (t70) REVERT: E 397 TRP cc_start: 0.9019 (t-100) cc_final: 0.8354 (t-100) REVERT: E 427 ASP cc_start: 0.8839 (m-30) cc_final: 0.7976 (m-30) REVERT: E 451 ARG cc_start: 0.9175 (ptp-170) cc_final: 0.8132 (mmt180) REVERT: E 464 LEU cc_start: 0.9255 (tp) cc_final: 0.8969 (tp) REVERT: E 471 TRP cc_start: 0.8313 (t60) cc_final: 0.7703 (t-100) REVERT: E 477 ARG cc_start: 0.8828 (mmm160) cc_final: 0.8439 (ttp80) REVERT: E 495 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9287 (tt) REVERT: F 6 THR cc_start: 0.8737 (p) cc_final: 0.8513 (p) REVERT: F 59 GLN cc_start: 0.9055 (mt0) cc_final: 0.8807 (mp10) REVERT: F 69 LEU cc_start: 0.9347 (mt) cc_final: 0.9065 (mt) REVERT: H 12 VAL cc_start: 0.8914 (m) cc_final: 0.8714 (p) REVERT: H 13 GLN cc_start: 0.8956 (mp10) cc_final: 0.8624 (mm-40) REVERT: H 29 PHE cc_start: 0.6956 (p90) cc_final: 0.6354 (p90) REVERT: H 32 PHE cc_start: 0.8377 (m-80) cc_final: 0.7631 (m-80) REVERT: H 34 MET cc_start: 0.7612 (mpp) cc_final: 0.6908 (mmt) REVERT: H 47 TRP cc_start: 0.9004 (t60) cc_final: 0.8106 (t60) REVERT: H 67 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6708 (mtp85) REVERT: H 80 CYS cc_start: 0.8251 (m) cc_final: 0.7544 (m) REVERT: H 82 GLN cc_start: 0.7383 (tp40) cc_final: 0.6765 (tm-30) REVERT: H 90 ASP cc_start: 0.8847 (m-30) cc_final: 0.7919 (m-30) REVERT: H 96 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.5855 (m) REVERT: H 100 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7141 (ttm170) REVERT: H 102 TYR cc_start: 0.8505 (p90) cc_final: 0.8195 (p90) REVERT: L 24 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7759 (ttm110) REVERT: L 28 ASN cc_start: 0.9178 (t0) cc_final: 0.8803 (m-40) REVERT: L 39 LYS cc_start: 0.7954 (mmmm) cc_final: 0.7647 (mmmm) REVERT: L 42 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8774 (mmtm) REVERT: L 62 PHE cc_start: 0.7898 (m-80) cc_final: 0.6680 (m-80) REVERT: L 79 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8012 (mm110) REVERT: L 83 PHE cc_start: 0.8248 (m-80) cc_final: 0.7729 (m-80) REVERT: L 89 GLN cc_start: 0.6729 (tm130) cc_final: 0.5889 (tm-30) REVERT: L 90 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6013 (ptm160) REVERT: L 92 PHE cc_start: 0.9049 (t80) cc_final: 0.8565 (t80) outliers start: 85 outliers final: 54 residues processed: 604 average time/residue: 0.0978 time to fit residues: 88.9678 Evaluate side-chains 607 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 543 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 187 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 HIS E 462 GLN ** F 7 HIS ** 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 = 0.3625 r_free = 0.3625 target = 0.125489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098978 restraints weight = 29324.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102565 restraints weight = 14318.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104987 restraints weight = 8828.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106640 restraints weight = 6252.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107737 restraints weight = 4891.385| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15194 Z= 0.123 Angle : 0.605 10.539 20631 Z= 0.306 Chirality : 0.043 0.205 2355 Planarity : 0.003 0.040 2606 Dihedral : 4.951 55.338 2151 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.03 % Allowed : 23.58 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1942 helix: 0.66 (0.24), residues: 471 sheet: -0.06 (0.24), residues: 521 loop : -0.77 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.025 0.002 TYR L 32 PHE 0.025 0.001 PHE C 450 TRP 0.015 0.001 TRP B 51 HIS 0.006 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15174) covalent geometry : angle 0.60417 / 0.31 (20588) SS BOND : bond 0.00553 / 0.27 ( 17) SS BOND : angle 0.94279 / 0.57 ( 34) hydrogen bonds : bond 0.03466 / 2.38 ( 621) hydrogen bonds : angle 5.01619 / 3.48 ( 1725) link_NAG-ASN : bond 0.00247 / 0.12 ( 3) link_NAG-ASN : angle 1.22149 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 573 time to evaluate : 0.450 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 42 ASP cc_start: 0.7814 (m-30) cc_final: 0.6707 (m-30) REVERT: A 48 MET cc_start: 0.8958 (ttp) cc_final: 0.8621 (ttp) REVERT: A 81 HIS cc_start: 0.7348 (t70) cc_final: 0.6835 (t70) REVERT: A 105 CYS cc_start: 0.7943 (m) cc_final: 0.6998 (m) REVERT: A 132 LYS cc_start: 0.8864 (mttt) cc_final: 0.8111 (mmtt) REVERT: A 142 PHE cc_start: 0.9056 (t80) cc_final: 0.8185 (t80) REVERT: A 155 TYR cc_start: 0.9436 (t80) cc_final: 0.8927 (t80) REVERT: A 178 LEU cc_start: 0.9041 (tp) cc_final: 0.7960 (tt) REVERT: A 185 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6793 (mm-30) REVERT: A 191 GLU cc_start: 0.8819 (mm-30) cc_final: 0.7983 (mm-30) REVERT: A 209 LYS cc_start: 0.8122 (tptt) cc_final: 0.7922 (ttmm) REVERT: A 215 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7101 (tpp80) REVERT: A 240 MET cc_start: 0.8921 (mtm) cc_final: 0.8377 (mtm) REVERT: A 241 GLU cc_start: 0.1449 (tt0) cc_final: 0.0301 (mt-10) REVERT: A 283 SER cc_start: 0.8660 (m) cc_final: 0.7295 (t) REVERT: A 298 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8443 (ttmt) REVERT: A 376 GLU cc_start: 0.9161 (tp30) cc_final: 0.8511 (tp30) REVERT: A 464 LEU cc_start: 0.8981 (mt) cc_final: 0.8075 (tt) REVERT: A 493 LEU cc_start: 0.9614 (mm) cc_final: 0.9170 (mm) REVERT: A 496 SER cc_start: 0.9325 (t) cc_final: 0.9083 (p) REVERT: B 28 TYR cc_start: 0.9390 (m-10) cc_final: 0.9155 (m-10) REVERT: B 42 TYR cc_start: 0.8989 (t80) cc_final: 0.8618 (t80) REVERT: B 58 MET cc_start: 0.8204 (tmm) cc_final: 0.7044 (tmm) REVERT: B 59 GLN cc_start: 0.8470 (pt0) cc_final: 0.7806 (pp30) REVERT: B 60 ARG cc_start: 0.9116 (ttm170) cc_final: 0.8630 (ttp-110) REVERT: C 8 ASN cc_start: 0.8858 (m110) cc_final: 0.8615 (m110) REVERT: C 9 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7941 (ptm160) REVERT: C 34 MET cc_start: 0.7625 (mtp) cc_final: 0.7400 (ttp) REVERT: C 45 MET cc_start: 0.8744 (tmm) cc_final: 0.7992 (tmm) REVERT: C 46 MET cc_start: 0.7978 (mtt) cc_final: 0.7602 (mtt) REVERT: C 55 GLU cc_start: 0.8364 (pm20) cc_final: 0.7400 (mp0) REVERT: C 61 TYR cc_start: 0.7811 (p90) cc_final: 0.7102 (p90) REVERT: C 77 MET cc_start: 0.7287 (ppp) cc_final: 0.7028 (ppp) REVERT: C 84 LYS cc_start: 0.8906 (tppt) cc_final: 0.8679 (tppt) REVERT: C 107 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7548 (tt) REVERT: C 240 MET cc_start: 0.8446 (mmp) cc_final: 0.8195 (mmm) REVERT: C 264 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 283 SER cc_start: 0.9044 (m) cc_final: 0.8622 (p) REVERT: C 302 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.4681 (p90) REVERT: C 327 LEU cc_start: 0.8706 (tp) cc_final: 0.8396 (tp) REVERT: C 346 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7616 (pt) REVERT: C 348 ASP cc_start: 0.8214 (t0) cc_final: 0.8004 (t70) REVERT: C 373 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7881 (mp) REVERT: C 379 PHE cc_start: 0.8098 (m-80) cc_final: 0.7818 (m-10) REVERT: C 406 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8239 (tppt) REVERT: C 444 GLN cc_start: 0.8986 (tp40) cc_final: 0.8345 (tm-30) REVERT: C 461 THR cc_start: 0.9300 (p) cc_final: 0.9040 (t) REVERT: C 471 TRP cc_start: 0.8373 (t60) cc_final: 0.7566 (t-100) REVERT: D 35 TRP cc_start: 0.8832 (t60) cc_final: 0.8205 (t60) REVERT: D 74 TYR cc_start: 0.8159 (m-80) cc_final: 0.7886 (m-80) REVERT: E 22 ASP cc_start: 0.6841 (t70) cc_final: 0.6331 (t70) REVERT: E 26 GLU cc_start: 0.8162 (tt0) cc_final: 0.7925 (tt0) REVERT: E 38 LYS cc_start: 0.9144 (mmtp) cc_final: 0.8606 (mmtm) REVERT: E 87 ASP cc_start: 0.8642 (t0) cc_final: 0.8039 (t0) REVERT: E 114 ASP cc_start: 0.7362 (m-30) cc_final: 0.7092 (m-30) REVERT: E 133 GLU cc_start: 0.5062 (mt-10) cc_final: 0.4647 (tt0) REVERT: E 149 VAL cc_start: 0.9201 (p) cc_final: 0.8968 (m) REVERT: E 169 ILE cc_start: 0.8551 (mm) cc_final: 0.8191 (tp) REVERT: E 182 GLU cc_start: 0.8621 (mp0) cc_final: 0.8245 (mp0) REVERT: E 191 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8286 (mm-30) REVERT: E 220 ASP cc_start: 0.7711 (m-30) cc_final: 0.7159 (m-30) REVERT: E 273 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7257 (tm-30) REVERT: E 280 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.7801 (ttpt) REVERT: E 396 HIS cc_start: 0.8697 (t-90) cc_final: 0.8128 (t-170) REVERT: E 397 TRP cc_start: 0.9008 (t-100) cc_final: 0.8319 (t-100) REVERT: E 427 ASP cc_start: 0.8805 (m-30) cc_final: 0.7983 (m-30) REVERT: E 451 ARG cc_start: 0.9181 (ptp-170) cc_final: 0.8137 (mmt180) REVERT: E 464 LEU cc_start: 0.9257 (tp) cc_final: 0.8962 (tp) REVERT: E 471 TRP cc_start: 0.8304 (t60) cc_final: 0.7703 (t60) REVERT: E 477 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8491 (ttp80) REVERT: E 478 ASP cc_start: 0.7838 (t0) cc_final: 0.7293 (t70) REVERT: E 495 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9334 (tt) REVERT: F 6 THR cc_start: 0.8798 (p) cc_final: 0.8592 (p) REVERT: F 27 ARG cc_start: 0.9101 (ptt-90) cc_final: 0.8883 (mtm180) REVERT: F 59 GLN cc_start: 0.9063 (mt0) cc_final: 0.8743 (mp10) REVERT: H 13 GLN cc_start: 0.8993 (mp10) cc_final: 0.8662 (mm-40) REVERT: H 29 PHE cc_start: 0.7108 (p90) cc_final: 0.6467 (p90) REVERT: H 32 PHE cc_start: 0.8320 (m-80) cc_final: 0.7692 (m-80) REVERT: H 34 MET cc_start: 0.7600 (mpp) cc_final: 0.6951 (mmt) REVERT: H 43 LYS cc_start: 0.8518 (tppt) cc_final: 0.8299 (tppt) REVERT: H 46 GLU cc_start: 0.8786 (tp30) cc_final: 0.8456 (tp30) REVERT: H 47 TRP cc_start: 0.9153 (t60) cc_final: 0.8283 (t60) REVERT: H 67 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6646 (mtp85) REVERT: H 80 CYS cc_start: 0.8414 (m) cc_final: 0.7652 (m) REVERT: H 82 GLN cc_start: 0.7345 (tp40) cc_final: 0.6754 (tm-30) REVERT: H 90 ASP cc_start: 0.8836 (m-30) cc_final: 0.7883 (m-30) REVERT: H 96 CYS cc_start: 0.6931 (OUTLIER) cc_final: 0.5852 (m) REVERT: H 102 TYR cc_start: 0.8494 (p90) cc_final: 0.7964 (p90) REVERT: L 39 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7908 (mmmm) REVERT: L 42 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8747 (mmtm) REVERT: L 62 PHE cc_start: 0.8180 (m-80) cc_final: 0.7363 (m-80) REVERT: L 79 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8019 (mm110) REVERT: L 83 PHE cc_start: 0.8206 (m-80) cc_final: 0.7711 (m-80) REVERT: L 89 GLN cc_start: 0.6864 (tm130) cc_final: 0.5917 (tm-30) REVERT: L 90 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5941 (ptm160) REVERT: L 92 PHE cc_start: 0.9038 (t80) cc_final: 0.8560 (t80) outliers start: 80 outliers final: 58 residues processed: 606 average time/residue: 0.0980 time to fit residues: 88.2104 Evaluate side-chains 622 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 555 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 27 optimal weight: 0.0040 chunk 107 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 ASN E 462 GLN ** F 7 HIS ** 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 = 0.3717 r_free = 0.3717 target = 0.131805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104375 restraints weight = 29696.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108080 restraints weight = 15073.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110560 restraints weight = 9513.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112251 restraints weight = 6868.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113336 restraints weight = 5447.832| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15194 Z= 0.131 Angle : 0.612 11.236 20631 Z= 0.306 Chirality : 0.043 0.210 2355 Planarity : 0.003 0.040 2606 Dihedral : 4.862 55.757 2151 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.66 % Allowed : 24.59 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1942 helix: 0.65 (0.24), residues: 471 sheet: -0.11 (0.23), residues: 535 loop : -0.75 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.023 0.002 TYR L 32 PHE 0.025 0.001 PHE C 450 TRP 0.014 0.001 TRP B 51 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15174) covalent geometry : angle 0.61151 / 0.31 (20588) SS BOND : bond 0.00538 / 0.29 ( 17) SS BOND : angle 0.77705 / 0.46 ( 34) hydrogen bonds : bond 0.03323 / 2.28 ( 621) hydrogen bonds : angle 4.89004 / 3.40 ( 1725) link_NAG-ASN : bond 0.00184 / 0.09 ( 3) link_NAG-ASN : angle 1.22967 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 562 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7765 (m-30) cc_final: 0.6735 (m-30) REVERT: A 48 MET cc_start: 0.8866 (ttp) cc_final: 0.8423 (ttp) REVERT: A 69 SER cc_start: 0.8924 (m) cc_final: 0.7862 (p) REVERT: A 81 HIS cc_start: 0.7364 (t70) cc_final: 0.6832 (t70) REVERT: A 87 ASP cc_start: 0.7868 (m-30) cc_final: 0.7449 (t0) REVERT: A 105 CYS cc_start: 0.8081 (m) cc_final: 0.7188 (m) REVERT: A 132 LYS cc_start: 0.8764 (mttt) cc_final: 0.8114 (mmtt) REVERT: A 142 PHE cc_start: 0.9086 (t80) cc_final: 0.8376 (t80) REVERT: A 155 TYR cc_start: 0.9438 (t80) cc_final: 0.8976 (t80) REVERT: A 185 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6790 (mm-30) REVERT: A 191 GLU cc_start: 0.8741 (mm-30) cc_final: 0.7724 (mm-30) REVERT: A 215 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7146 (tpp80) REVERT: A 240 MET cc_start: 0.8821 (mtm) cc_final: 0.8304 (mtm) REVERT: A 241 GLU cc_start: 0.1661 (tt0) cc_final: 0.0887 (pt0) REVERT: A 273 GLU cc_start: 0.6245 (tp30) cc_final: 0.5946 (tp30) REVERT: A 283 SER cc_start: 0.7537 (m) cc_final: 0.6472 (t) REVERT: A 298 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8473 (ttmt) REVERT: A 376 GLU cc_start: 0.9045 (tp30) cc_final: 0.8520 (tp30) REVERT: A 413 LYS cc_start: 0.9302 (tppp) cc_final: 0.9031 (ttmt) REVERT: A 457 MET cc_start: 0.7971 (mtp) cc_final: 0.7378 (ttm) REVERT: A 464 LEU cc_start: 0.9016 (mt) cc_final: 0.8111 (tt) REVERT: A 493 LEU cc_start: 0.9654 (mm) cc_final: 0.9187 (mm) REVERT: A 496 SER cc_start: 0.9339 (t) cc_final: 0.9125 (p) REVERT: B 28 TYR cc_start: 0.9349 (m-10) cc_final: 0.9136 (m-10) REVERT: B 42 TYR cc_start: 0.9034 (t80) cc_final: 0.8583 (t80) REVERT: B 58 MET cc_start: 0.8220 (tmm) cc_final: 0.7016 (tmm) REVERT: B 59 GLN cc_start: 0.8503 (pt0) cc_final: 0.7763 (pp30) REVERT: B 60 ARG cc_start: 0.9130 (ttm170) cc_final: 0.8644 (ttp-110) REVERT: C 8 ASN cc_start: 0.8842 (m110) cc_final: 0.8627 (m110) REVERT: C 9 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8036 (ptm160) REVERT: C 45 MET cc_start: 0.8815 (tmm) cc_final: 0.8512 (tmm) REVERT: C 46 MET cc_start: 0.7759 (mtt) cc_final: 0.7473 (mtt) REVERT: C 48 MET cc_start: 0.8068 (tmm) cc_final: 0.7560 (tmm) REVERT: C 55 GLU cc_start: 0.8284 (pm20) cc_final: 0.7770 (mp0) REVERT: C 61 TYR cc_start: 0.7662 (p90) cc_final: 0.6950 (p90) REVERT: C 77 MET cc_start: 0.7378 (ppp) cc_final: 0.7174 (ppp) REVERT: C 84 LYS cc_start: 0.8993 (tppt) cc_final: 0.8741 (tppt) REVERT: C 107 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7749 (tt) REVERT: C 155 TYR cc_start: 0.9324 (t80) cc_final: 0.8977 (t80) REVERT: C 264 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8844 (tm-30) REVERT: C 283 SER cc_start: 0.9053 (m) cc_final: 0.8684 (p) REVERT: C 296 GLN cc_start: 0.8513 (pt0) cc_final: 0.7254 (pm20) REVERT: C 302 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.4717 (p90) REVERT: C 346 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7639 (pt) REVERT: C 373 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8011 (mp) REVERT: C 379 PHE cc_start: 0.7552 (m-80) cc_final: 0.7186 (m-10) REVERT: C 406 LYS cc_start: 0.8724 (ttpp) cc_final: 0.8277 (tppt) REVERT: C 444 GLN cc_start: 0.8904 (tp40) cc_final: 0.8311 (tm-30) REVERT: C 461 THR cc_start: 0.9309 (p) cc_final: 0.9050 (t) REVERT: C 471 TRP cc_start: 0.8415 (t60) cc_final: 0.7603 (t-100) REVERT: D 35 TRP cc_start: 0.8714 (t60) cc_final: 0.8220 (t60) REVERT: D 52 MET cc_start: 0.9042 (tpp) cc_final: 0.8826 (tpp) REVERT: E 22 ASP cc_start: 0.6910 (t70) cc_final: 0.6369 (t70) REVERT: E 26 GLU cc_start: 0.8150 (tt0) cc_final: 0.7650 (tt0) REVERT: E 33 ILE cc_start: 0.9425 (pp) cc_final: 0.9222 (pp) REVERT: E 38 LYS cc_start: 0.9163 (mmtp) cc_final: 0.8703 (mmtm) REVERT: E 55 GLU cc_start: 0.8468 (mp0) cc_final: 0.8096 (mp0) REVERT: E 58 SER cc_start: 0.9065 (m) cc_final: 0.8615 (p) REVERT: E 59 TYR cc_start: 0.8148 (m-10) cc_final: 0.5785 (m-10) REVERT: E 133 GLU cc_start: 0.4831 (mt-10) cc_final: 0.4254 (tt0) REVERT: E 149 VAL cc_start: 0.9203 (p) cc_final: 0.8990 (m) REVERT: E 182 GLU cc_start: 0.8503 (mp0) cc_final: 0.8247 (mp0) REVERT: E 191 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8398 (mm-30) REVERT: E 209 LYS cc_start: 0.8199 (tppt) cc_final: 0.7728 (mmmt) REVERT: E 273 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7289 (tm-30) REVERT: E 280 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7681 (ttpt) REVERT: E 396 HIS cc_start: 0.8759 (t-90) cc_final: 0.8042 (t70) REVERT: E 397 TRP cc_start: 0.9047 (t-100) cc_final: 0.8325 (t-100) REVERT: E 427 ASP cc_start: 0.8847 (m-30) cc_final: 0.8040 (m-30) REVERT: E 451 ARG cc_start: 0.9207 (ptp-170) cc_final: 0.8169 (mmt180) REVERT: E 464 LEU cc_start: 0.9262 (tp) cc_final: 0.8964 (tp) REVERT: E 471 TRP cc_start: 0.8343 (t60) cc_final: 0.7767 (t60) REVERT: E 477 ARG cc_start: 0.8780 (mmm160) cc_final: 0.8488 (ttp80) REVERT: E 495 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9417 (tt) REVERT: F 20 MET cc_start: 0.7627 (mmm) cc_final: 0.7169 (mmm) REVERT: F 27 ARG cc_start: 0.9128 (ptt-90) cc_final: 0.8891 (mtm180) REVERT: F 59 GLN cc_start: 0.9013 (mt0) cc_final: 0.8797 (mp10) REVERT: H 13 GLN cc_start: 0.9170 (mp10) cc_final: 0.8862 (mm-40) REVERT: H 29 PHE cc_start: 0.7229 (p90) cc_final: 0.6612 (p90) REVERT: H 32 PHE cc_start: 0.8252 (m-80) cc_final: 0.7633 (m-80) REVERT: H 34 MET cc_start: 0.7714 (mpp) cc_final: 0.7076 (mmt) REVERT: H 43 LYS cc_start: 0.8437 (tppt) cc_final: 0.7866 (mmmt) REVERT: H 45 LEU cc_start: 0.8810 (mt) cc_final: 0.8490 (mp) REVERT: H 46 GLU cc_start: 0.8768 (tp30) cc_final: 0.8523 (tp30) REVERT: H 47 TRP cc_start: 0.9207 (t60) cc_final: 0.8325 (t60) REVERT: H 67 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6865 (mtp85) REVERT: H 70 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8330 (tp) REVERT: H 80 CYS cc_start: 0.8509 (m) cc_final: 0.7492 (m) REVERT: H 82 GLN cc_start: 0.7372 (tp40) cc_final: 0.6488 (tm-30) REVERT: H 90 ASP cc_start: 0.8867 (m-30) cc_final: 0.7978 (m-30) REVERT: H 96 CYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6608 (m) REVERT: H 100 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7004 (ttm170) REVERT: H 102 TYR cc_start: 0.8527 (p90) cc_final: 0.7945 (p90) REVERT: L 23 CYS cc_start: 0.6169 (t) cc_final: 0.5962 (t) REVERT: L 39 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8046 (mmmm) REVERT: L 42 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8874 (mmtm) REVERT: L 62 PHE cc_start: 0.8317 (m-80) cc_final: 0.7310 (m-80) REVERT: L 79 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8025 (mm110) REVERT: L 83 PHE cc_start: 0.8178 (m-80) cc_final: 0.7692 (m-80) REVERT: L 85 THR cc_start: 0.9153 (m) cc_final: 0.8619 (p) REVERT: L 89 GLN cc_start: 0.7085 (tm130) cc_final: 0.6449 (tm-30) REVERT: L 90 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5920 (ptm160) outliers start: 90 outliers final: 70 residues processed: 594 average time/residue: 0.1021 time to fit residues: 90.6085 Evaluate side-chains 633 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 553 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 122 optimal weight: 0.0370 chunk 130 optimal weight: 9.9990 chunk 133 optimal weight: 0.0980 chunk 186 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 overall best weight: 4.6264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN E 462 GLN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 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 = 0.3672 r_free = 0.3672 target = 0.128219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101445 restraints weight = 29328.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104934 restraints weight = 14642.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107300 restraints weight = 9164.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108897 restraints weight = 6567.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109978 restraints weight = 5184.612| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15194 Z= 0.246 Angle : 0.665 12.317 20631 Z= 0.339 Chirality : 0.044 0.213 2355 Planarity : 0.004 0.045 2606 Dihedral : 5.168 54.488 2151 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.54 % Allowed : 24.78 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 1942 helix: 0.66 (0.25), residues: 459 sheet: -0.22 (0.24), residues: 496 loop : -0.88 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.025 0.002 TYR L 32 PHE 0.026 0.002 PHE C 450 TRP 0.017 0.002 TRP F 51 HIS 0.007 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.25 (15174) covalent geometry : angle 0.66384 / 0.34 (20588) SS BOND : bond 0.00360 / 0.18 ( 17) SS BOND : angle 0.82316 / 0.48 ( 34) hydrogen bonds : bond 0.03576 / 2.44 ( 621) hydrogen bonds : angle 5.09238 / 3.52 ( 1725) link_NAG-ASN : bond 0.00143 / 0.07 ( 3) link_NAG-ASN : angle 1.48877 / 1.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 545 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7923 (m-30) cc_final: 0.6924 (m-30) REVERT: A 48 MET cc_start: 0.9062 (ttp) cc_final: 0.8422 (ttp) REVERT: A 81 HIS cc_start: 0.7547 (t70) cc_final: 0.6939 (t70) REVERT: A 87 ASP cc_start: 0.7947 (m-30) cc_final: 0.7384 (t0) REVERT: A 105 CYS cc_start: 0.8526 (m) cc_final: 0.7891 (m) REVERT: A 114 ASP cc_start: 0.7924 (t0) cc_final: 0.7215 (t0) REVERT: A 132 LYS cc_start: 0.8956 (mttt) cc_final: 0.8250 (mmtt) REVERT: A 142 PHE cc_start: 0.9036 (t80) cc_final: 0.8292 (t80) REVERT: A 155 TYR cc_start: 0.9501 (t80) cc_final: 0.8883 (t80) REVERT: A 178 LEU cc_start: 0.9048 (tp) cc_final: 0.8110 (tp) REVERT: A 185 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 191 GLU cc_start: 0.8818 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 240 MET cc_start: 0.8996 (mtm) cc_final: 0.8427 (mtm) REVERT: A 241 GLU cc_start: 0.2313 (tt0) cc_final: 0.1084 (pt0) REVERT: A 298 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8455 (ttmt) REVERT: A 376 GLU cc_start: 0.9102 (tp30) cc_final: 0.8519 (tp30) REVERT: A 464 LEU cc_start: 0.9030 (mt) cc_final: 0.8121 (tt) REVERT: A 493 LEU cc_start: 0.9677 (mm) cc_final: 0.9164 (mm) REVERT: A 495 LEU cc_start: 0.9437 (mt) cc_final: 0.9157 (mt) REVERT: A 496 SER cc_start: 0.9586 (t) cc_final: 0.9305 (p) REVERT: B 42 TYR cc_start: 0.9155 (t80) cc_final: 0.8806 (t80) REVERT: B 58 MET cc_start: 0.8416 (tmm) cc_final: 0.7140 (tmm) REVERT: B 59 GLN cc_start: 0.8471 (pt0) cc_final: 0.7738 (pp30) REVERT: B 60 ARG cc_start: 0.9166 (ttm170) cc_final: 0.8589 (ttm-80) REVERT: C 46 MET cc_start: 0.7952 (mtt) cc_final: 0.7582 (mtt) REVERT: C 55 GLU cc_start: 0.8377 (pm20) cc_final: 0.7412 (mp0) REVERT: C 61 TYR cc_start: 0.7906 (p90) cc_final: 0.7628 (p90) REVERT: C 84 LYS cc_start: 0.9140 (tppt) cc_final: 0.8761 (tppt) REVERT: C 107 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7786 (tt) REVERT: C 155 TYR cc_start: 0.9389 (t80) cc_final: 0.9009 (t80) REVERT: C 264 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8936 (tm-30) REVERT: C 283 SER cc_start: 0.9165 (m) cc_final: 0.8747 (p) REVERT: C 287 LYS cc_start: 0.9279 (tttm) cc_final: 0.8766 (tttp) REVERT: C 302 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.5049 (p90) REVERT: C 346 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7319 (pt) REVERT: C 373 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7857 (mp) REVERT: C 379 PHE cc_start: 0.7849 (m-80) cc_final: 0.7474 (m-10) REVERT: C 406 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8289 (tppt) REVERT: C 444 GLN cc_start: 0.8977 (tp40) cc_final: 0.8410 (tm-30) REVERT: C 461 THR cc_start: 0.9387 (p) cc_final: 0.9177 (t) REVERT: C 471 TRP cc_start: 0.8454 (t60) cc_final: 0.7642 (t-100) REVERT: D 35 TRP cc_start: 0.8854 (t60) cc_final: 0.8288 (t60) REVERT: D 52 MET cc_start: 0.9088 (tpp) cc_final: 0.8715 (tpp) REVERT: E 22 ASP cc_start: 0.6938 (t70) cc_final: 0.6467 (t70) REVERT: E 38 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8598 (mmtm) REVERT: E 55 GLU cc_start: 0.8548 (mp0) cc_final: 0.8152 (mp0) REVERT: E 58 SER cc_start: 0.9105 (m) cc_final: 0.8507 (p) REVERT: E 87 ASP cc_start: 0.8559 (t0) cc_final: 0.8143 (t0) REVERT: E 96 VAL cc_start: 0.9526 (t) cc_final: 0.9233 (p) REVERT: E 133 GLU cc_start: 0.5399 (mt-10) cc_final: 0.4637 (tt0) REVERT: E 167 PHE cc_start: 0.9449 (p90) cc_final: 0.8838 (p90) REVERT: E 182 GLU cc_start: 0.8576 (mp0) cc_final: 0.8311 (mp0) REVERT: E 209 LYS cc_start: 0.8270 (tppt) cc_final: 0.7781 (mmmt) REVERT: E 220 ASP cc_start: 0.7898 (m-30) cc_final: 0.7580 (m-30) REVERT: E 280 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8456 (ttpt) REVERT: E 383 TYR cc_start: 0.8128 (m-80) cc_final: 0.7180 (m-80) REVERT: E 396 HIS cc_start: 0.8801 (t-90) cc_final: 0.8090 (t70) REVERT: E 427 ASP cc_start: 0.8834 (m-30) cc_final: 0.7986 (m-30) REVERT: E 451 ARG cc_start: 0.9227 (ptp-170) cc_final: 0.8138 (mmt180) REVERT: E 471 TRP cc_start: 0.8410 (t60) cc_final: 0.7706 (t-100) REVERT: E 477 ARG cc_start: 0.8825 (mmm160) cc_final: 0.8451 (ttp80) REVERT: E 478 ASP cc_start: 0.7888 (t0) cc_final: 0.7454 (t70) REVERT: F 27 ARG cc_start: 0.9139 (ptt-90) cc_final: 0.8761 (mtm180) REVERT: F 59 GLN cc_start: 0.9049 (mt0) cc_final: 0.8749 (mp10) REVERT: H 29 PHE cc_start: 0.7264 (p90) cc_final: 0.6659 (p90) REVERT: H 32 PHE cc_start: 0.8384 (m-80) cc_final: 0.7491 (m-80) REVERT: H 34 MET cc_start: 0.7873 (mpp) cc_final: 0.7166 (mmt) REVERT: H 47 TRP cc_start: 0.9264 (t60) cc_final: 0.8179 (t60) REVERT: H 67 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6824 (mtp85) REVERT: H 80 CYS cc_start: 0.8476 (m) cc_final: 0.7624 (m) REVERT: H 82 GLN cc_start: 0.6789 (tp40) cc_final: 0.6012 (tm-30) REVERT: H 90 ASP cc_start: 0.8884 (m-30) cc_final: 0.7983 (m-30) REVERT: H 96 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6010 (m) REVERT: H 100 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7435 (ttm170) REVERT: H 102 TYR cc_start: 0.8658 (p90) cc_final: 0.8174 (p90) REVERT: L 23 CYS cc_start: 0.6204 (t) cc_final: 0.5933 (t) REVERT: L 39 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7981 (mmmm) REVERT: L 48 ILE cc_start: 0.8957 (mp) cc_final: 0.8567 (mt) REVERT: L 62 PHE cc_start: 0.8413 (m-80) cc_final: 0.7448 (m-80) REVERT: L 79 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8043 (mm110) REVERT: L 83 PHE cc_start: 0.8162 (m-80) cc_final: 0.7644 (m-80) REVERT: L 85 THR cc_start: 0.9285 (m) cc_final: 0.8837 (p) REVERT: L 89 GLN cc_start: 0.7066 (tm130) cc_final: 0.6329 (tm-30) REVERT: L 90 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6108 (ptm160) REVERT: L 98 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8228 (t80) outliers start: 104 outliers final: 85 residues processed: 588 average time/residue: 0.0940 time to fit residues: 82.9906 Evaluate side-chains 624 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 530 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 83 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 462 GLN ** F 7 HIS ** 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 = 0.3704 r_free = 0.3704 target = 0.130852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103232 restraints weight = 29847.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106858 restraints weight = 15295.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109310 restraints weight = 9741.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110986 restraints weight = 7078.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112074 restraints weight = 5640.839| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15194 Z= 0.150 Angle : 0.654 12.746 20631 Z= 0.325 Chirality : 0.043 0.195 2355 Planarity : 0.004 0.041 2606 Dihedral : 5.006 55.868 2151 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.47 % Allowed : 27.30 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.19), residues: 1942 helix: 0.70 (0.24), residues: 471 sheet: -0.16 (0.24), residues: 527 loop : -0.89 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 24 TYR 0.031 0.002 TYR B 28 PHE 0.025 0.001 PHE C 450 TRP 0.019 0.001 TRP F 51 HIS 0.005 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15174) covalent geometry : angle 0.65331 / 0.33 (20588) SS BOND : bond 0.00256 / 0.12 ( 17) SS BOND : angle 0.77397 / 0.45 ( 34) hydrogen bonds : bond 0.03321 / 2.27 ( 621) hydrogen bonds : angle 4.85874 / 3.38 ( 1725) link_NAG-ASN : bond 0.00158 / 0.08 ( 3) link_NAG-ASN : angle 1.26085 / 0.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 548 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7825 (m-30) cc_final: 0.6854 (m-30) REVERT: A 46 MET cc_start: 0.8785 (mmm) cc_final: 0.8581 (mmm) REVERT: A 69 SER cc_start: 0.8806 (m) cc_final: 0.7798 (p) REVERT: A 81 HIS cc_start: 0.7399 (t70) cc_final: 0.6930 (t70) REVERT: A 87 ASP cc_start: 0.7957 (m-30) cc_final: 0.7399 (t0) REVERT: A 105 CYS cc_start: 0.8597 (m) cc_final: 0.7884 (m) REVERT: A 132 LYS cc_start: 0.8852 (mttt) cc_final: 0.8177 (mmtt) REVERT: A 142 PHE cc_start: 0.8992 (t80) cc_final: 0.8320 (t80) REVERT: A 155 TYR cc_start: 0.9429 (t80) cc_final: 0.8890 (t80) REVERT: A 178 LEU cc_start: 0.9025 (tp) cc_final: 0.8109 (tp) REVERT: A 185 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6798 (mm-30) REVERT: A 191 GLU cc_start: 0.8782 (mm-30) cc_final: 0.7954 (mm-30) REVERT: A 240 MET cc_start: 0.8884 (mtm) cc_final: 0.8297 (mtm) REVERT: A 280 LYS cc_start: 0.8604 (ttpt) cc_final: 0.7895 (ttmm) REVERT: A 298 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8424 (ttmt) REVERT: A 376 GLU cc_start: 0.9002 (tp30) cc_final: 0.8446 (tp30) REVERT: A 464 LEU cc_start: 0.9028 (mt) cc_final: 0.8134 (tt) REVERT: A 493 LEU cc_start: 0.9688 (mm) cc_final: 0.9183 (mm) REVERT: A 495 LEU cc_start: 0.9431 (mt) cc_final: 0.9156 (mt) REVERT: A 496 SER cc_start: 0.9562 (t) cc_final: 0.9318 (p) REVERT: B 42 TYR cc_start: 0.9100 (t80) cc_final: 0.8520 (t80) REVERT: B 58 MET cc_start: 0.8474 (tmm) cc_final: 0.7443 (tmm) REVERT: B 59 GLN cc_start: 0.8561 (pt0) cc_final: 0.7813 (pp30) REVERT: B 60 ARG cc_start: 0.9164 (ttm170) cc_final: 0.8573 (ttm-80) REVERT: C 45 MET cc_start: 0.8799 (tmm) cc_final: 0.8466 (tmm) REVERT: C 46 MET cc_start: 0.7789 (mtt) cc_final: 0.7355 (mtt) REVERT: C 55 GLU cc_start: 0.8315 (pm20) cc_final: 0.7455 (mp0) REVERT: C 61 TYR cc_start: 0.8008 (p90) cc_final: 0.7549 (p90) REVERT: C 77 MET cc_start: 0.7294 (ppp) cc_final: 0.7081 (ppp) REVERT: C 84 LYS cc_start: 0.9155 (tppt) cc_final: 0.8796 (tppt) REVERT: C 101 TRP cc_start: 0.9191 (m-10) cc_final: 0.8587 (m-10) REVERT: C 107 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7848 (tt) REVERT: C 155 TYR cc_start: 0.9358 (t80) cc_final: 0.9046 (t80) REVERT: C 158 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8920 (mm110) REVERT: C 264 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8813 (tm-30) REVERT: C 283 SER cc_start: 0.9064 (m) cc_final: 0.8680 (p) REVERT: C 287 LYS cc_start: 0.9284 (tttm) cc_final: 0.8764 (tttp) REVERT: C 302 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.4856 (p90) REVERT: C 346 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7425 (pt) REVERT: C 373 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8029 (mp) REVERT: C 379 PHE cc_start: 0.7715 (m-80) cc_final: 0.7333 (m-10) REVERT: C 406 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8288 (tppt) REVERT: C 444 GLN cc_start: 0.8863 (tp40) cc_final: 0.8372 (tm-30) REVERT: C 461 THR cc_start: 0.9356 (p) cc_final: 0.9048 (t) REVERT: C 471 TRP cc_start: 0.8475 (t60) cc_final: 0.7594 (t-100) REVERT: D 35 TRP cc_start: 0.8576 (t60) cc_final: 0.8376 (t60) REVERT: D 52 MET cc_start: 0.9059 (tpp) cc_final: 0.8651 (tpp) REVERT: E 22 ASP cc_start: 0.6894 (t70) cc_final: 0.6455 (t70) REVERT: E 26 GLU cc_start: 0.8105 (tt0) cc_final: 0.7893 (tt0) REVERT: E 38 LYS cc_start: 0.9251 (mmtp) cc_final: 0.8753 (mmtm) REVERT: E 58 SER cc_start: 0.9028 (m) cc_final: 0.8479 (p) REVERT: E 96 VAL cc_start: 0.9499 (t) cc_final: 0.9184 (p) REVERT: E 133 GLU cc_start: 0.5274 (mt-10) cc_final: 0.4579 (tt0) REVERT: E 167 PHE cc_start: 0.9356 (p90) cc_final: 0.8856 (p90) REVERT: E 182 GLU cc_start: 0.8535 (mp0) cc_final: 0.8281 (mp0) REVERT: E 191 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8428 (mm-30) REVERT: E 209 LYS cc_start: 0.8312 (tppt) cc_final: 0.7684 (tptm) REVERT: E 220 ASP cc_start: 0.7837 (m-30) cc_final: 0.7336 (m-30) REVERT: E 241 GLU cc_start: 0.8379 (tp30) cc_final: 0.8029 (tp30) REVERT: E 294 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8960 (mmmm) REVERT: E 359 ASN cc_start: 0.9341 (p0) cc_final: 0.9139 (p0) REVERT: E 396 HIS cc_start: 0.8817 (t-90) cc_final: 0.8190 (t70) REVERT: E 397 TRP cc_start: 0.9044 (t-100) cc_final: 0.8327 (t-100) REVERT: E 427 ASP cc_start: 0.8832 (m-30) cc_final: 0.7958 (m-30) REVERT: E 451 ARG cc_start: 0.9229 (ptp-170) cc_final: 0.8122 (mmt180) REVERT: E 471 TRP cc_start: 0.8386 (t60) cc_final: 0.7776 (t60) REVERT: E 477 ARG cc_start: 0.8796 (mmm160) cc_final: 0.8493 (ttp80) REVERT: F 15 LYS cc_start: 0.9480 (mmmm) cc_final: 0.8724 (mmtm) REVERT: F 20 MET cc_start: 0.7655 (mmm) cc_final: 0.7105 (mmm) REVERT: F 27 ARG cc_start: 0.9129 (ptt-90) cc_final: 0.8724 (mtm180) REVERT: F 59 GLN cc_start: 0.9015 (mt0) cc_final: 0.8705 (mp10) REVERT: F 63 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: H 29 PHE cc_start: 0.7257 (p90) cc_final: 0.6638 (p90) REVERT: H 32 PHE cc_start: 0.8346 (m-80) cc_final: 0.7475 (m-80) REVERT: H 34 MET cc_start: 0.7864 (mpp) cc_final: 0.7117 (mmt) REVERT: H 43 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8428 (mmmt) REVERT: H 47 TRP cc_start: 0.9200 (t60) cc_final: 0.8240 (t60) REVERT: H 67 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6892 (mtp85) REVERT: H 80 CYS cc_start: 0.8552 (m) cc_final: 0.7594 (m) REVERT: H 82 GLN cc_start: 0.6899 (tp40) cc_final: 0.6093 (tm-30) REVERT: H 90 ASP cc_start: 0.8887 (m-30) cc_final: 0.7914 (m-30) REVERT: H 96 CYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6854 (m) REVERT: H 100 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7424 (ttm170) REVERT: H 102 TYR cc_start: 0.8579 (p90) cc_final: 0.8065 (p90) REVERT: L 23 CYS cc_start: 0.6236 (t) cc_final: 0.5984 (t) REVERT: L 39 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8010 (mmmm) REVERT: L 48 ILE cc_start: 0.8971 (mp) cc_final: 0.8626 (mt) REVERT: L 62 PHE cc_start: 0.8338 (m-80) cc_final: 0.7466 (m-80) REVERT: L 79 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7914 (mp10) REVERT: L 83 PHE cc_start: 0.8138 (m-80) cc_final: 0.7583 (m-80) REVERT: L 85 THR cc_start: 0.9285 (m) cc_final: 0.8812 (p) REVERT: L 89 GLN cc_start: 0.6970 (tm130) cc_final: 0.6312 (tm-30) REVERT: L 90 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6075 (ptm160) REVERT: L 98 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8004 (t80) outliers start: 87 outliers final: 70 residues processed: 580 average time/residue: 0.0969 time to fit residues: 84.6672 Evaluate side-chains 618 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 539 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 181 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 462 GLN ** F 7 HIS ** 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 = 0.3741 r_free = 0.3741 target = 0.134191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106821 restraints weight = 29546.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110597 restraints weight = 14707.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113200 restraints weight = 9194.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114892 restraints weight = 6570.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115985 restraints weight = 5194.316| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15194 Z= 0.127 Angle : 0.655 13.225 20631 Z= 0.323 Chirality : 0.043 0.192 2355 Planarity : 0.003 0.040 2606 Dihedral : 4.863 57.405 2151 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.91 % Allowed : 27.67 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1942 helix: 0.66 (0.24), residues: 471 sheet: -0.17 (0.23), residues: 551 loop : -0.83 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 24 TYR 0.020 0.002 TYR D 42 PHE 0.024 0.001 PHE C 450 TRP 0.032 0.001 TRP C 225 HIS 0.005 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15174) covalent geometry : angle 0.65455 / 0.32 (20588) SS BOND : bond 0.00171 / 0.09 ( 17) SS BOND : angle 0.70000 / 0.40 ( 34) hydrogen bonds : bond 0.03298 / 2.24 ( 621) hydrogen bonds : angle 4.79294 / 3.33 ( 1725) link_NAG-ASN : bond 0.00204 / 0.10 ( 3) link_NAG-ASN : angle 1.21069 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 562 time to evaluate : 0.491 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 42 ASP cc_start: 0.7826 (m-30) cc_final: 0.6803 (m-30) REVERT: A 69 SER cc_start: 0.8912 (m) cc_final: 0.7860 (p) REVERT: A 81 HIS cc_start: 0.7281 (t70) cc_final: 0.6845 (t70) REVERT: A 87 ASP cc_start: 0.7931 (m-30) cc_final: 0.7487 (t0) REVERT: A 105 CYS cc_start: 0.8540 (m) cc_final: 0.7843 (m) REVERT: A 132 LYS cc_start: 0.8739 (mttt) cc_final: 0.8090 (mmtt) REVERT: A 142 PHE cc_start: 0.9038 (t80) cc_final: 0.8468 (t80) REVERT: A 155 TYR cc_start: 0.9399 (t80) cc_final: 0.8921 (t80) REVERT: A 178 LEU cc_start: 0.9005 (tp) cc_final: 0.8035 (tp) REVERT: A 185 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6753 (mm-30) REVERT: A 191 GLU cc_start: 0.8827 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 215 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7137 (tpp80) REVERT: A 240 MET cc_start: 0.8873 (mtm) cc_final: 0.8272 (mtm) REVERT: A 280 LYS cc_start: 0.8534 (ttpt) cc_final: 0.7836 (ptmm) REVERT: A 283 SER cc_start: 0.7707 (m) cc_final: 0.6557 (t) REVERT: A 298 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8447 (ttmt) REVERT: A 376 GLU cc_start: 0.9017 (tp30) cc_final: 0.8404 (tp30) REVERT: A 418 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8796 (tt) REVERT: A 457 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: A 468 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8691 (mm) REVERT: A 493 LEU cc_start: 0.9681 (mm) cc_final: 0.9164 (mm) REVERT: A 495 LEU cc_start: 0.9419 (mt) cc_final: 0.9150 (mt) REVERT: A 496 SER cc_start: 0.9551 (t) cc_final: 0.9297 (p) REVERT: B 35 TRP cc_start: 0.8950 (t60) cc_final: 0.8550 (t60) REVERT: B 36 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9186 (mm) REVERT: B 42 TYR cc_start: 0.9058 (t80) cc_final: 0.8563 (t80) REVERT: B 58 MET cc_start: 0.8623 (tmm) cc_final: 0.7301 (tmm) REVERT: B 59 GLN cc_start: 0.8598 (pt0) cc_final: 0.7892 (pp30) REVERT: B 60 ARG cc_start: 0.9152 (ttm170) cc_final: 0.8560 (ttm-80) REVERT: C 46 MET cc_start: 0.7709 (mtt) cc_final: 0.7463 (mtt) REVERT: C 55 GLU cc_start: 0.8304 (pm20) cc_final: 0.7421 (mp0) REVERT: C 77 MET cc_start: 0.7280 (ppp) cc_final: 0.7040 (ppp) REVERT: C 84 LYS cc_start: 0.9162 (tppt) cc_final: 0.8777 (tppt) REVERT: C 101 TRP cc_start: 0.9176 (m-10) cc_final: 0.8580 (m-10) REVERT: C 107 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7764 (tt) REVERT: C 155 TYR cc_start: 0.9280 (t80) cc_final: 0.8997 (t80) REVERT: C 158 GLN cc_start: 0.9358 (mm-40) cc_final: 0.8914 (mm110) REVERT: C 196 ILE cc_start: 0.8874 (tt) cc_final: 0.8481 (pt) REVERT: C 264 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 283 SER cc_start: 0.9068 (m) cc_final: 0.8697 (p) REVERT: C 287 LYS cc_start: 0.9287 (tttm) cc_final: 0.8762 (tttp) REVERT: C 302 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.4752 (p90) REVERT: C 346 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7450 (pt) REVERT: C 373 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8017 (mp) REVERT: C 379 PHE cc_start: 0.7687 (m-80) cc_final: 0.7314 (m-10) REVERT: C 406 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8268 (tppt) REVERT: C 444 GLN cc_start: 0.8837 (tp40) cc_final: 0.8348 (tm-30) REVERT: C 461 THR cc_start: 0.9336 (p) cc_final: 0.9049 (t) REVERT: C 471 TRP cc_start: 0.8570 (t60) cc_final: 0.7728 (t-100) REVERT: D 35 TRP cc_start: 0.8477 (t60) cc_final: 0.8163 (t60) REVERT: D 52 MET cc_start: 0.9022 (tpp) cc_final: 0.8536 (tpp) REVERT: E 22 ASP cc_start: 0.6963 (t70) cc_final: 0.6436 (t70) REVERT: E 26 GLU cc_start: 0.8243 (tt0) cc_final: 0.7791 (tt0) REVERT: E 38 LYS cc_start: 0.9211 (mmtp) cc_final: 0.8744 (mmtm) REVERT: E 58 SER cc_start: 0.9099 (m) cc_final: 0.8528 (p) REVERT: E 61 TYR cc_start: 0.8429 (p90) cc_final: 0.8080 (p90) REVERT: E 87 ASP cc_start: 0.8599 (t0) cc_final: 0.8028 (t0) REVERT: E 133 GLU cc_start: 0.4987 (mt-10) cc_final: 0.4180 (tt0) REVERT: E 167 PHE cc_start: 0.9328 (p90) cc_final: 0.8792 (p90) REVERT: E 182 GLU cc_start: 0.8512 (mp0) cc_final: 0.8257 (mp0) REVERT: E 191 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8442 (mm-30) REVERT: E 209 LYS cc_start: 0.8277 (tppt) cc_final: 0.7733 (mmmt) REVERT: E 241 GLU cc_start: 0.8448 (tp30) cc_final: 0.8106 (tp30) REVERT: E 294 LYS cc_start: 0.9279 (mmmm) cc_final: 0.9008 (mmmm) REVERT: E 396 HIS cc_start: 0.8752 (t-90) cc_final: 0.8204 (t-170) REVERT: E 397 TRP cc_start: 0.9041 (t-100) cc_final: 0.8384 (t-100) REVERT: E 427 ASP cc_start: 0.8790 (m-30) cc_final: 0.8103 (m-30) REVERT: E 451 ARG cc_start: 0.9216 (ptp-170) cc_final: 0.8135 (mmt180) REVERT: E 471 TRP cc_start: 0.8368 (t60) cc_final: 0.7799 (t60) REVERT: E 477 ARG cc_start: 0.8784 (mmm160) cc_final: 0.8504 (ttp80) REVERT: E 478 ASP cc_start: 0.7887 (t0) cc_final: 0.7464 (t70) REVERT: F 15 LYS cc_start: 0.9360 (mmmm) cc_final: 0.8552 (mmtm) REVERT: F 27 ARG cc_start: 0.9058 (ptt-90) cc_final: 0.8628 (mtm180) REVERT: F 51 TRP cc_start: 0.7673 (t-100) cc_final: 0.7312 (t-100) REVERT: F 59 GLN cc_start: 0.9049 (mt0) cc_final: 0.8711 (mp10) REVERT: F 63 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: H 29 PHE cc_start: 0.7179 (p90) cc_final: 0.6647 (p90) REVERT: H 32 PHE cc_start: 0.8289 (m-80) cc_final: 0.7503 (m-80) REVERT: H 34 MET cc_start: 0.7814 (mpp) cc_final: 0.7095 (mmt) REVERT: H 43 LYS cc_start: 0.8540 (mmmm) cc_final: 0.8315 (mmmt) REVERT: H 47 TRP cc_start: 0.9182 (t60) cc_final: 0.8251 (t60) REVERT: H 67 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6813 (mtp85) REVERT: H 80 CYS cc_start: 0.8486 (m) cc_final: 0.7585 (m) REVERT: H 81 LEU cc_start: 0.8258 (tt) cc_final: 0.8057 (tt) REVERT: H 82 GLN cc_start: 0.6776 (tp40) cc_final: 0.5978 (tm-30) REVERT: H 90 ASP cc_start: 0.8843 (m-30) cc_final: 0.7886 (m-30) REVERT: H 96 CYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6756 (m) REVERT: H 102 TYR cc_start: 0.8526 (p90) cc_final: 0.7963 (p90) REVERT: L 4 MET cc_start: 0.5819 (mmm) cc_final: 0.5358 (tpt) REVERT: L 39 LYS cc_start: 0.8321 (mmmm) cc_final: 0.8025 (mmmm) REVERT: L 48 ILE cc_start: 0.8924 (mp) cc_final: 0.8619 (mt) REVERT: L 62 PHE cc_start: 0.8323 (m-80) cc_final: 0.7317 (m-80) REVERT: L 70 ASP cc_start: 0.8745 (p0) cc_final: 0.7971 (t0) REVERT: L 79 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7884 (mp10) REVERT: L 83 PHE cc_start: 0.8328 (m-80) cc_final: 0.7511 (m-80) REVERT: L 85 THR cc_start: 0.9252 (m) cc_final: 0.8795 (p) REVERT: L 89 GLN cc_start: 0.6916 (tm130) cc_final: 0.6222 (tm-30) REVERT: L 90 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6213 (tmm-80) REVERT: L 98 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8116 (t80) outliers start: 78 outliers final: 57 residues processed: 592 average time/residue: 0.0998 time to fit residues: 89.1068 Evaluate side-chains 610 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 540 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 172 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 148 optimal weight: 0.4980 chunk 10 optimal weight: 0.0020 chunk 177 optimal weight: 9.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN E 258 GLN E 462 GLN ** F 7 HIS ** 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 = 0.3776 r_free = 0.3776 target = 0.137786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110226 restraints weight = 29355.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114093 restraints weight = 14717.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116692 restraints weight = 9213.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118464 restraints weight = 6617.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119670 restraints weight = 5226.555| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15194 Z= 0.124 Angle : 0.680 14.459 20631 Z= 0.333 Chirality : 0.044 0.226 2355 Planarity : 0.004 0.043 2606 Dihedral : 4.793 57.292 2151 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.90 % Allowed : 28.99 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1942 helix: 0.64 (0.24), residues: 471 sheet: -0.15 (0.23), residues: 547 loop : -0.81 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 354 TYR 0.041 0.002 TYR C 61 PHE 0.023 0.001 PHE E 435 TRP 0.037 0.001 TRP C 225 HIS 0.005 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (15174) covalent geometry : angle 0.67935 / 0.33 (20588) SS BOND : bond 0.00115 / 0.06 ( 17) SS BOND : angle 0.80572 / 0.50 ( 34) hydrogen bonds : bond 0.03247 / 2.19 ( 621) hydrogen bonds : angle 4.78802 / 3.33 ( 1725) link_NAG-ASN : bond 0.00205 / 0.10 ( 3) link_NAG-ASN : angle 1.19025 / 0.80 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 560 time to evaluate : 0.456 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 42 ASP cc_start: 0.8015 (m-30) cc_final: 0.7232 (m-30) REVERT: A 46 MET cc_start: 0.8762 (mmm) cc_final: 0.8473 (mmm) REVERT: A 48 MET cc_start: 0.8809 (ttp) cc_final: 0.8092 (ttp) REVERT: A 69 SER cc_start: 0.8710 (m) cc_final: 0.7728 (p) REVERT: A 81 HIS cc_start: 0.7162 (t70) cc_final: 0.6754 (t70) REVERT: A 105 CYS cc_start: 0.8590 (m) cc_final: 0.7824 (m) REVERT: A 132 LYS cc_start: 0.8602 (mttt) cc_final: 0.8194 (mmtt) REVERT: A 142 PHE cc_start: 0.9014 (t80) cc_final: 0.8713 (t80) REVERT: A 155 TYR cc_start: 0.9366 (t80) cc_final: 0.8953 (t80) REVERT: A 178 LEU cc_start: 0.8976 (tp) cc_final: 0.8459 (tp) REVERT: A 185 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6994 (mm-30) REVERT: A 191 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 215 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7117 (tpp80) REVERT: A 240 MET cc_start: 0.8791 (mtm) cc_final: 0.8215 (mtm) REVERT: A 283 SER cc_start: 0.7706 (m) cc_final: 0.6593 (t) REVERT: A 298 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8602 (ttmt) REVERT: A 346 LEU cc_start: 0.8804 (mm) cc_final: 0.8299 (pt) REVERT: A 376 GLU cc_start: 0.8995 (tp30) cc_final: 0.8380 (tp30) REVERT: A 413 LYS cc_start: 0.9332 (tppp) cc_final: 0.9046 (ttmt) REVERT: A 418 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8807 (tt) REVERT: A 464 LEU cc_start: 0.9023 (mt) cc_final: 0.7940 (tt) REVERT: A 468 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 493 LEU cc_start: 0.9687 (mm) cc_final: 0.9239 (mm) REVERT: A 495 LEU cc_start: 0.9399 (mt) cc_final: 0.9135 (mt) REVERT: A 496 SER cc_start: 0.9525 (t) cc_final: 0.9296 (p) REVERT: B 35 TRP cc_start: 0.8917 (t60) cc_final: 0.8431 (t60) REVERT: B 42 TYR cc_start: 0.8986 (t80) cc_final: 0.8446 (t80) REVERT: B 58 MET cc_start: 0.8593 (tmm) cc_final: 0.7240 (tmm) REVERT: B 59 GLN cc_start: 0.8589 (pt0) cc_final: 0.7874 (pp30) REVERT: B 60 ARG cc_start: 0.9157 (ttm170) cc_final: 0.8730 (ttp-110) REVERT: C 55 GLU cc_start: 0.8320 (pm20) cc_final: 0.7426 (mp0) REVERT: C 77 MET cc_start: 0.7268 (ppp) cc_final: 0.7022 (ppp) REVERT: C 84 LYS cc_start: 0.8954 (tppt) cc_final: 0.8548 (tppt) REVERT: C 101 TRP cc_start: 0.9169 (m-10) cc_final: 0.8556 (m-10) REVERT: C 107 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7723 (tt) REVERT: C 155 TYR cc_start: 0.9263 (t80) cc_final: 0.9019 (t80) REVERT: C 158 GLN cc_start: 0.9373 (mm-40) cc_final: 0.8902 (mm110) REVERT: C 259 GLU cc_start: 0.8807 (tt0) cc_final: 0.8202 (tt0) REVERT: C 264 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8754 (tm-30) REVERT: C 283 SER cc_start: 0.9024 (m) cc_final: 0.8648 (p) REVERT: C 302 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.4507 (p90) REVERT: C 346 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7447 (pt) REVERT: C 379 PHE cc_start: 0.7662 (m-80) cc_final: 0.7288 (m-10) REVERT: C 406 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8257 (tppt) REVERT: C 444 GLN cc_start: 0.8801 (tp40) cc_final: 0.8327 (tm-30) REVERT: C 461 THR cc_start: 0.9315 (p) cc_final: 0.9011 (t) REVERT: C 471 TRP cc_start: 0.8519 (t60) cc_final: 0.7673 (t-100) REVERT: D 38 ARG cc_start: 0.8901 (tpp80) cc_final: 0.8514 (ttm-80) REVERT: D 52 MET cc_start: 0.8935 (tpp) cc_final: 0.8598 (tpp) REVERT: D 74 TYR cc_start: 0.7595 (m-80) cc_final: 0.7335 (m-80) REVERT: E 22 ASP cc_start: 0.7095 (t70) cc_final: 0.6587 (t70) REVERT: E 26 GLU cc_start: 0.8058 (tt0) cc_final: 0.7286 (tt0) REVERT: E 28 ASP cc_start: 0.8238 (t70) cc_final: 0.7829 (t70) REVERT: E 38 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8704 (mmtm) REVERT: E 87 ASP cc_start: 0.8597 (t0) cc_final: 0.8031 (t0) REVERT: E 114 ASP cc_start: 0.6729 (m-30) cc_final: 0.6351 (m-30) REVERT: E 133 GLU cc_start: 0.4909 (mt-10) cc_final: 0.4127 (tt0) REVERT: E 137 TYR cc_start: 0.8494 (m-80) cc_final: 0.8081 (m-80) REVERT: E 167 PHE cc_start: 0.9315 (p90) cc_final: 0.8852 (p90) REVERT: E 182 GLU cc_start: 0.8474 (mp0) cc_final: 0.8233 (mp0) REVERT: E 185 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7603 (mm-30) REVERT: E 191 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8510 (mm-30) REVERT: E 209 LYS cc_start: 0.8308 (tppt) cc_final: 0.7740 (mmmt) REVERT: E 229 GLU cc_start: 0.8548 (tp30) cc_final: 0.8328 (tp30) REVERT: E 241 GLU cc_start: 0.8381 (tp30) cc_final: 0.8038 (tp30) REVERT: E 258 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7917 (mm110) REVERT: E 396 HIS cc_start: 0.8753 (t-90) cc_final: 0.8220 (t-170) REVERT: E 397 TRP cc_start: 0.9035 (t-100) cc_final: 0.8393 (t-100) REVERT: E 427 ASP cc_start: 0.8805 (m-30) cc_final: 0.8226 (m-30) REVERT: E 451 ARG cc_start: 0.9218 (ptp-170) cc_final: 0.8130 (mmt180) REVERT: E 471 TRP cc_start: 0.8290 (t60) cc_final: 0.7853 (t60) REVERT: E 477 ARG cc_start: 0.8809 (mmm160) cc_final: 0.8552 (ttp80) REVERT: E 478 ASP cc_start: 0.7875 (t0) cc_final: 0.7462 (t70) REVERT: F 15 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8451 (mmtm) REVERT: F 27 ARG cc_start: 0.9020 (ptt-90) cc_final: 0.8605 (mtm180) REVERT: F 59 GLN cc_start: 0.9011 (mt0) cc_final: 0.8666 (mp10) REVERT: F 63 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: H 29 PHE cc_start: 0.7019 (p90) cc_final: 0.6499 (p90) REVERT: H 32 PHE cc_start: 0.8273 (m-80) cc_final: 0.7456 (m-80) REVERT: H 34 MET cc_start: 0.7599 (mpp) cc_final: 0.7158 (mmt) REVERT: H 47 TRP cc_start: 0.9090 (t60) cc_final: 0.8077 (t60) REVERT: H 67 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6880 (mtp85) REVERT: H 80 CYS cc_start: 0.8543 (m) cc_final: 0.7676 (m) REVERT: H 81 LEU cc_start: 0.8391 (tt) cc_final: 0.8172 (tt) REVERT: H 82 GLN cc_start: 0.6820 (tp40) cc_final: 0.6174 (tm-30) REVERT: H 90 ASP cc_start: 0.8795 (m-30) cc_final: 0.7873 (m-30) REVERT: H 96 CYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6918 (m) REVERT: H 100 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7222 (ttm-80) REVERT: H 102 TYR cc_start: 0.8504 (p90) cc_final: 0.7976 (p90) REVERT: L 4 MET cc_start: 0.5769 (mmm) cc_final: 0.4839 (tpt) REVERT: L 24 ARG cc_start: 0.8516 (ttm110) cc_final: 0.7597 (ttm110) REVERT: L 39 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8078 (mmmm) REVERT: L 48 ILE cc_start: 0.8828 (mp) cc_final: 0.8544 (mt) REVERT: L 70 ASP cc_start: 0.8744 (p0) cc_final: 0.7988 (t0) REVERT: L 79 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7897 (mp10) REVERT: L 83 PHE cc_start: 0.8335 (m-80) cc_final: 0.7516 (m-80) REVERT: L 85 THR cc_start: 0.9264 (m) cc_final: 0.8767 (p) REVERT: L 89 GLN cc_start: 0.6833 (tm130) cc_final: 0.6211 (tm-30) REVERT: L 90 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6155 (tmm160) REVERT: L 98 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8021 (t80) outliers start: 62 outliers final: 46 residues processed: 585 average time/residue: 0.0984 time to fit residues: 86.3463 Evaluate side-chains 598 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 541 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 133 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 50 optimal weight: 0.0470 chunk 95 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN C 47 ASN E 462 GLN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104867 restraints weight = 29764.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108498 restraints weight = 15257.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110969 restraints weight = 9712.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112619 restraints weight = 7033.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113761 restraints weight = 5598.990| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15194 Z= 0.176 Angle : 0.697 13.386 20631 Z= 0.343 Chirality : 0.044 0.230 2355 Planarity : 0.004 0.046 2606 Dihedral : 4.861 55.880 2151 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.34 % Allowed : 29.18 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1942 helix: 0.70 (0.25), residues: 474 sheet: -0.20 (0.23), residues: 542 loop : -0.86 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.024 0.002 TYR L 86 PHE 0.029 0.002 PHE E 108 TRP 0.038 0.002 TRP C 225 HIS 0.005 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (15174) covalent geometry : angle 0.69611 / 0.34 (20588) SS BOND : bond 0.00290 / 0.16 ( 17) SS BOND : angle 0.76254 / 0.46 ( 34) hydrogen bonds : bond 0.03260 / 2.22 ( 621) hydrogen bonds : angle 4.80860 / 3.34 ( 1725) link_NAG-ASN : bond 0.00038 / 0.02 ( 3) link_NAG-ASN : angle 1.26442 / 0.86 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.76 seconds wall clock time: 44 minutes 38.45 seconds (2678.45 seconds total)