Starting phenix.real_space_refine on Wed Oct 28 09:38:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sh6_54889/10_2026/9sh6_54889_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sh6_54889/10_2026/9sh6_54889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sh6_54889/10_2026/9sh6_54889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sh6_54889/10_2026/9sh6_54889.map" model { file = "/net/cci-nas-00/data/ceres_data/9sh6_54889/10_2026/9sh6_54889_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sh6_54889/10_2026/9sh6_54889_trim.cif" } resolution = 2.77 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= 0.002 sd= 0.034 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: 5 Type Number sf(0) Gaussians S 74 5.16 5 C 9612 2.51 5 N 2410 2.21 5 O 2790 1.98 5 H 12302 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27188 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4701 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4669 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 235 Classifications: {'peptide': 13} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "I" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 235 Classifications: {'peptide': 13} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "G" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 6, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 4758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 4758 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 10, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3155 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 4758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 4758 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 10, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3155 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 6, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 189 Unusual residues: {'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 189 Unusual residues: {'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.23, per 1000 atoms: 0.19 Number of scatterers: 27188 At special positions: 0 Unit cell: (136.74, 102.34, 154.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 O 2790 8.00 N 2410 7.00 C 9612 6.00 H 12302 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG B 501 " - " ASN B 25 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 963.7 milliseconds 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 20 sheets defined 45.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 37 through 73 removed outlier: 3.786A pdb=" N LEU B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 121 through 154 removed outlier: 4.182A pdb=" N VAL B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 195 removed outlier: 3.617A pdb=" N MET B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 236 removed outlier: 3.996A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 268 removed outlier: 3.557A pdb=" N ILE B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 304 removed outlier: 4.146A pdb=" N VAL B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 37 through 73 removed outlier: 3.832A pdb=" N LEU A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 154 removed outlier: 4.204A pdb=" N VAL A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 195 Processing helix chain 'A' and resid 201 through 236 removed outlier: 4.218A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 268 removed outlier: 3.559A pdb=" N ILE A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 276 removed outlier: 4.095A pdb=" N VAL A 276 " --> pdb=" O GLY A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 277 through 304 removed outlier: 4.848A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'G' and resid 31 through 46 Processing helix chain 'G' and resid 52 through 65 removed outlier: 3.813A pdb=" N ALA G 56 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 65 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 84 through 98 removed outlier: 3.761A pdb=" N LEU G 90 " --> pdb=" O PHE G 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS G 95 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 58 Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.515A pdb=" N MET C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'E' and resid 16 through 40 removed outlier: 3.553A pdb=" N ASN E 20 " --> pdb=" O PRO E 16 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 63 removed outlier: 3.515A pdb=" N VAL E 57 " --> pdb=" O GLY E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.923A pdb=" N LYS E 329 " --> pdb=" O GLU E 326 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP E 330 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N HIS E 332 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU E 335 " --> pdb=" O HIS E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 374 removed outlier: 3.891A pdb=" N ILE E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN E 374 " --> pdb=" O ASP E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 379 removed outlier: 3.582A pdb=" N PHE E 378 " --> pdb=" O SER E 375 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS E 379 " --> pdb=" O LYS E 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 375 through 379' Processing helix chain 'E' and resid 390 through 398 removed outlier: 3.919A pdb=" N LYS E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 431 removed outlier: 3.641A pdb=" N LEU E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 428 " --> pdb=" O GLU E 424 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 430 " --> pdb=" O ILE E 426 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN E 431 " --> pdb=" O PHE E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 469 removed outlier: 3.850A pdb=" N PHE E 452 " --> pdb=" O GLN E 448 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 58 removed outlier: 3.557A pdb=" N ARG F 43 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 335 through 342 removed outlier: 3.737A pdb=" N LYS F 340 " --> pdb=" O PRO F 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 40 removed outlier: 3.695A pdb=" N GLU D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 66 removed outlier: 3.549A pdb=" N VAL D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.880A pdb=" N LYS D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N HIS D 332 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 335 " --> pdb=" O HIS D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 374 Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.852A pdb=" N LYS D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 397 Processing helix chain 'D' and resid 416 through 431 removed outlier: 4.051A pdb=" N LEU D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 430 " --> pdb=" O ILE D 426 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 469 removed outlier: 3.770A pdb=" N PHE D 452 " --> pdb=" O GLN D 448 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 46 Processing helix chain 'H' and resid 52 through 67 removed outlier: 3.876A pdb=" N ALA H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR H 67 " --> pdb=" O TYR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 84 through 98 removed outlier: 3.906A pdb=" N LYS H 95 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.857A pdb=" N ARG B 318 " --> pdb=" O GLU F 388 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE F 383 " --> pdb=" O ASP F 377 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP F 377 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY F 385 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N CYS F 373 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET F 364 " --> pdb=" O TRP F 376 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER F 354 " --> pdb=" O CYS F 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.786A pdb=" N LYS C 83 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C 396 " --> pdb=" O GLY C 409 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 95 through 100 removed outlier: 3.684A pdb=" N ASP C 97 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 118 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 139 through 142 removed outlier: 6.582A pdb=" N CYS C 158 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C 176 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 160 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 184 through 189 removed outlier: 3.760A pdb=" N ASP C 186 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 204 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU C 217 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU C 206 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 228 through 229 removed outlier: 3.818A pdb=" N PHE C 243 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.825A pdb=" N GLY C 288 " --> pdb=" O ASN C 274 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 276 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 286 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE C 278 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET C 296 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 306 " --> pdb=" O MET C 296 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP C 298 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 352 through 357 removed outlier: 6.700A pdb=" N CYS C 367 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU C 355 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR C 365 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE C 357 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU C 363 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 364 " --> pdb=" O TRP C 376 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS C 373 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY C 385 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP C 377 " --> pdb=" O ILE C 383 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 383 " --> pdb=" O ASP C 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.830A pdb=" N PHE E 308 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.546A pdb=" N VAL E 340 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE E 386 " --> pdb=" O VAL E 340 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE E 342 " --> pdb=" O PHE E 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 88 removed outlier: 5.765A pdb=" N SER F 419 " --> pdb=" O PRO F 84 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE F 86 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY F 396 " --> pdb=" O GLY F 409 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 95 through 100 removed outlier: 6.837A pdb=" N ALA F 110 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE F 98 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU F 108 " --> pdb=" O PHE F 98 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP F 100 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG F 106 " --> pdb=" O TRP F 100 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 128 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP F 120 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS F 126 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 139 through 142 removed outlier: 3.504A pdb=" N VAL F 149 " --> pdb=" O TYR F 161 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG F 162 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL F 173 " --> pdb=" O ARG F 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 187 through 191 removed outlier: 3.515A pdb=" N THR F 190 " --> pdb=" O HIS F 194 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N CYS F 204 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLU F 217 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU F 206 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 228 through 229 removed outlier: 3.631A pdb=" N ALA F 229 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE F 243 " --> pdb=" O TRP F 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 276 through 278 removed outlier: 3.578A pdb=" N ARG F 277 " --> pdb=" O VAL F 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.866A pdb=" N PHE D 308 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.557A pdb=" N VAL D 340 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N PHE D 386 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE D 342 " --> pdb=" O PHE D 386 " (cutoff:3.500A) 737 hydrogen bonds defined for protein. 2109 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: 6.71 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12274 1.03 - 1.23: 67 1.23 - 1.42: 6214 1.42 - 1.62: 8823 1.62 - 1.82: 120 Bond restraints: 27498 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.450 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.25e+00 ... (remaining 27493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.54: 48249 10.54 - 21.07: 38 21.07 - 31.61: 115 31.61 - 42.14: 132 42.14 - 52.68: 12 Bond angle restraints: 48546 Sorted by residual: angle pdb=" C ASP F 256 " pdb=" N SER F 257 " pdb=" H SER F 257 " ideal model delta sigma weight residual 125.01 72.33 52.68 3.00e+00 1.11e-01 3.08e+02 angle pdb=" CA SER F 399 " pdb=" N SER F 399 " pdb=" H SER F 399 " ideal model delta sigma weight residual 113.53 61.39 52.13 3.00e+00 1.11e-01 3.02e+02 angle pdb=" CA SER F 257 " pdb=" N SER F 257 " pdb=" H SER F 257 " ideal model delta sigma weight residual 114.71 62.77 51.94 3.00e+00 1.11e-01 3.00e+02 angle pdb=" CA SER C 399 " pdb=" N SER C 399 " pdb=" H SER C 399 " ideal model delta sigma weight residual 113.53 61.85 51.67 3.00e+00 1.11e-01 2.97e+02 angle pdb=" C ARG F 398 " pdb=" N SER F 399 " pdb=" H SER F 399 " ideal model delta sigma weight residual 123.83 73.33 50.49 3.00e+00 1.11e-01 2.83e+02 ... (remaining 48541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 12279 17.82 - 35.64: 1198 35.64 - 53.47: 310 53.47 - 71.29: 67 71.29 - 89.11: 14 Dihedral angle restraints: 13868 sinusoidal: 7336 harmonic: 6532 Sorted by residual: dihedral pdb=" CA LEU E 387 " pdb=" C LEU E 387 " pdb=" N ASN E 388 " pdb=" CA ASN E 388 " ideal model delta harmonic sigma weight residual 180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU D 387 " pdb=" C LEU D 387 " pdb=" N ASN D 388 " pdb=" CA ASN D 388 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" C ILE G 60 " pdb=" N ILE G 60 " pdb=" CA ILE G 60 " pdb=" CB ILE G 60 " ideal model delta harmonic sigma weight residual -122.00 -133.89 11.89 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 13865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 2443 0.352 - 0.704: 25 0.704 - 1.057: 0 1.057 - 1.409: 3 1.409 - 1.761: 23 Chirality restraints: 2494 Sorted by residual: chirality pdb=" CG LEU E 385 " pdb=" CB LEU E 385 " pdb=" CD1 LEU E 385 " pdb=" CD2 LEU E 385 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.75e+01 chirality pdb=" CB ILE F 195 " pdb=" CA ILE F 195 " pdb=" CG1 ILE F 195 " pdb=" CG2 ILE F 195 " both_signs ideal model delta sigma weight residual False 2.64 0.89 1.75 2.00e-01 2.50e+01 7.67e+01 chirality pdb=" CG LEU C 228 " pdb=" CB LEU C 228 " pdb=" CD1 LEU C 228 " pdb=" CD2 LEU C 228 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.52e+01 ... (remaining 2491 not shown) Planarity restraints: 4173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 308 " 0.008 2.00e-02 2.50e+03 1.15e-02 3.99e+00 pdb=" CG PHE D 308 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE D 308 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 308 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE D 308 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 308 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 308 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE D 308 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE D 308 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE D 308 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE D 308 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE D 308 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 258 " -0.174 9.50e-02 1.11e+02 5.82e-02 3.94e+00 pdb=" NE ARG F 258 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 258 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG F 258 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 258 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG F 258 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG F 258 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG F 258 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG F 258 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 337 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C GLN C 337 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN C 337 " -0.013 2.00e-02 2.50e+03 pdb=" N THR C 338 " -0.011 2.00e-02 2.50e+03 ... (remaining 4170 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 814 2.16 - 2.77: 44897 2.77 - 3.38: 67935 3.38 - 3.99: 88955 3.99 - 4.60: 139554 Nonbonded interactions: 342155 Sorted by model distance: nonbonded pdb=" H GLN F 127 " pdb=" HA GLN F 127 " model vdw 1.547 1.816 nonbonded pdb=" H GLN C 127 " pdb=" HA GLN C 127 " model vdw 1.559 1.816 nonbonded pdb=" H LEU F 206 " pdb=" HA LEU F 206 " model vdw 1.589 1.816 nonbonded pdb=" H ILE G 51 " pdb=" HA ILE G 51 " model vdw 1.591 1.816 nonbonded pdb=" H LEU K 6 " pdb=" HA LEU K 6 " model vdw 1.591 1.816 ... (remaining 342150 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 'B' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 78 through 160 or (resid \ 161 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 162 through 506)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.410 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.104 15198 Z= 0.269 Angle : 1.035 28.282 20741 Z= 0.523 Chirality : 0.176 1.761 2494 Planarity : 0.005 0.076 2553 Dihedral : 15.499 89.109 5803 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.99 % Allowed : 20.29 % Favored : 78.71 % Cbeta Deviations : 0.60 % 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: 0.27 (0.20), residues: 1910 helix: 2.76 (0.19), residues: 770 sheet: -0.85 (0.32), residues: 292 loop : -2.03 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 258 TYR 0.032 0.002 TYR G 63 PHE 0.032 0.002 PHE D 308 TRP 0.013 0.002 TRP C 119 HIS 0.010 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 (15196) covalent geometry : angle 1.03533 / 0.52 (20735) hydrogen bonds : bond 0.20007 / 13.28 ( 737) hydrogen bonds : angle 5.31977 / 3.85 ( 2109) link_NAG-ASN : bond 0.00100 / 0.05 ( 2) link_NAG-ASN : angle 1.28084 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 330 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 VAL cc_start: 0.8348 (t) cc_final: 0.8094 (p) REVERT: B 267 SER cc_start: 0.8553 (t) cc_final: 0.8327 (p) REVERT: B 301 ASN cc_start: 0.8373 (m110) cc_final: 0.8085 (m-40) REVERT: A 151 LYS cc_start: 0.8348 (ttmm) cc_final: 0.8080 (ttmm) REVERT: A 191 VAL cc_start: 0.8162 (t) cc_final: 0.7870 (p) REVERT: A 197 SER cc_start: 0.8295 (m) cc_final: 0.7983 (t) REVERT: A 301 ASN cc_start: 0.8366 (m110) cc_final: 0.8117 (m110) REVERT: C 211 LYS cc_start: 0.8436 (mttt) cc_final: 0.8140 (mtpt) REVERT: C 337 GLN cc_start: 0.8133 (tp40) cc_final: 0.7862 (mm-40) REVERT: E 28 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7366 (mt-10) REVERT: E 356 ASP cc_start: 0.8137 (t0) cc_final: 0.7845 (t0) REVERT: E 362 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7157 (tmm) REVERT: F 123 SER cc_start: 0.7941 (m) cc_final: 0.7534 (p) REVERT: F 211 LYS cc_start: 0.8245 (mttt) cc_final: 0.7915 (mtpt) REVERT: D 356 ASP cc_start: 0.8063 (t0) cc_final: 0.7760 (t0) REVERT: D 403 ARG cc_start: 0.8017 (ttt90) cc_final: 0.7679 (ttt90) outliers start: 15 outliers final: 11 residues processed: 337 average time/residue: 0.9079 time to fit residues: 342.8716 Evaluate side-chains 337 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 325 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 GLN C 112 GLN C 167 ASN E 309 ASN F 167 ASN D 374 ASN H 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100201 restraints weight = 57410.761| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.11 r_work: 0.3235 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15198 Z= 0.240 Angle : 0.914 26.928 20741 Z= 0.460 Chirality : 0.172 1.740 2494 Planarity : 0.004 0.048 2553 Dihedral : 6.941 60.006 2827 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.52 % Allowed : 19.03 % Favored : 78.45 % Cbeta Deviations : 0.22 % 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 (0.20), residues: 1910 helix: 2.99 (0.18), residues: 776 sheet: -0.92 (0.31), residues: 308 loop : -2.03 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 106 TYR 0.015 0.001 TYR B 106 PHE 0.014 0.002 PHE D 393 TRP 0.021 0.002 TRP C 119 HIS 0.004 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (15196) covalent geometry : angle 0.91349 / 0.46 (20735) hydrogen bonds : bond 0.08557 / 5.68 ( 737) hydrogen bonds : angle 4.26362 / 3.12 ( 2109) link_NAG-ASN : bond 0.00161 / 0.08 ( 2) link_NAG-ASN : angle 1.66720 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 ASN cc_start: 0.8403 (m110) cc_final: 0.8136 (m110) REVERT: A 151 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8146 (ttmm) REVERT: A 301 ASN cc_start: 0.8507 (m110) cc_final: 0.8299 (m110) REVERT: C 211 LYS cc_start: 0.8541 (mttt) cc_final: 0.8152 (mtpt) REVERT: C 337 GLN cc_start: 0.8270 (tp40) cc_final: 0.8009 (mm-40) REVERT: E 28 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7268 (mt-10) REVERT: E 356 ASP cc_start: 0.8076 (t0) cc_final: 0.7715 (t0) REVERT: F 123 SER cc_start: 0.7885 (m) cc_final: 0.7465 (p) REVERT: F 211 LYS cc_start: 0.8314 (mttt) cc_final: 0.8013 (mtpt) REVERT: D 356 ASP cc_start: 0.8069 (t0) cc_final: 0.7757 (t0) REVERT: D 403 ARG cc_start: 0.7997 (ttt90) cc_final: 0.7596 (ttt90) REVERT: D 410 GLN cc_start: 0.7913 (mp10) cc_final: 0.7568 (mm-40) outliers start: 38 outliers final: 17 residues processed: 341 average time/residue: 0.8946 time to fit residues: 343.5240 Evaluate side-chains 335 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 318 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [97, 87, 56, 5, 105, 174, 83, 43, 163, 52, 125] chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 GLN C 112 GLN C 167 ASN E 309 ASN F 112 GLN F 167 ASN H 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099326 restraints weight = 57476.030| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.11 r_work: 0.3223 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15198 Z= 0.258 Angle : 0.918 26.525 20741 Z= 0.463 Chirality : 0.172 1.740 2494 Planarity : 0.004 0.051 2553 Dihedral : 6.600 60.173 2813 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.18 % Allowed : 18.37 % Favored : 78.45 % Cbeta Deviations : 0.22 % 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: 0.25 (0.20), residues: 1910 helix: 2.74 (0.18), residues: 794 sheet: -0.81 (0.31), residues: 312 loop : -2.23 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 398 TYR 0.013 0.002 TYR B 106 PHE 0.017 0.002 PHE E 393 TRP 0.022 0.002 TRP C 119 HIS 0.005 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 (15196) covalent geometry : angle 0.91721 / 0.46 (20735) hydrogen bonds : bond 0.08775 / 5.83 ( 737) hydrogen bonds : angle 4.21955 / 3.10 ( 2109) link_NAG-ASN : bond 0.00169 / 0.09 ( 2) link_NAG-ASN : angle 1.81991 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 368 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7872 (mtt) REVERT: B 301 ASN cc_start: 0.8420 (m110) cc_final: 0.8190 (m110) REVERT: A 121 SER cc_start: 0.8141 (t) cc_final: 0.7904 (p) REVERT: A 151 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8183 (ttmm) REVERT: A 218 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.6943 (mmt) REVERT: A 301 ASN cc_start: 0.8536 (m110) cc_final: 0.8333 (m110) REVERT: I 13 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.5623 (m-10) REVERT: C 211 LYS cc_start: 0.8491 (mttt) cc_final: 0.8137 (mtpt) REVERT: C 221 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8122 (t-90) REVERT: C 337 GLN cc_start: 0.8296 (tp40) cc_final: 0.8030 (mm-40) REVERT: E 28 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7286 (mt-10) REVERT: E 305 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: E 356 ASP cc_start: 0.8082 (t0) cc_final: 0.7721 (t0) REVERT: F 123 SER cc_start: 0.7935 (m) cc_final: 0.7590 (p) REVERT: F 211 LYS cc_start: 0.8316 (mttt) cc_final: 0.7984 (mtpt) REVERT: D 356 ASP cc_start: 0.8097 (t0) cc_final: 0.7771 (t0) REVERT: D 403 ARG cc_start: 0.8004 (ttt90) cc_final: 0.7650 (ttt90) REVERT: D 410 GLN cc_start: 0.7954 (mp10) cc_final: 0.7558 (mm-40) outliers start: 48 outliers final: 24 residues processed: 343 average time/residue: 0.8777 time to fit residues: 339.5964 Evaluate side-chains 352 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain I residue 13 TYR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [171, 175, 93, 1, 155, 113, 131, 121, 164, 29, 99] chunk 171 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 GLN A 118 GLN C 112 GLN C 167 ASN E 309 ASN F 112 GLN F 167 ASN D 309 ASN H 85 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100181 restraints weight = 57118.462| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.11 r_work: 0.3237 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15198 Z= 0.202 Angle : 0.894 26.662 20741 Z= 0.449 Chirality : 0.171 1.731 2494 Planarity : 0.004 0.047 2553 Dihedral : 6.414 59.920 2813 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.98 % Allowed : 18.97 % Favored : 78.05 % Cbeta Deviations : 0.22 % 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: 0.42 (0.20), residues: 1910 helix: 2.92 (0.18), residues: 792 sheet: -0.57 (0.33), residues: 294 loop : -2.23 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 398 TYR 0.014 0.001 TYR B 106 PHE 0.015 0.001 PHE E 393 TRP 0.018 0.001 TRP C 119 HIS 0.004 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (15196) covalent geometry : angle 0.89368 / 0.45 (20735) hydrogen bonds : bond 0.08032 / 5.34 ( 737) hydrogen bonds : angle 4.08266 / 3.00 ( 2109) link_NAG-ASN : bond 0.00147 / 0.08 ( 2) link_NAG-ASN : angle 1.78880 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7772 (mtt) REVERT: B 301 ASN cc_start: 0.8393 (m110) cc_final: 0.8142 (m110) REVERT: A 151 LYS cc_start: 0.8413 (ttmm) cc_final: 0.8152 (ttmm) REVERT: A 301 ASN cc_start: 0.8527 (m110) cc_final: 0.8311 (m110) REVERT: I 13 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.5589 (m-10) REVERT: G 64 THR cc_start: 0.8959 (t) cc_final: 0.8756 (m) REVERT: C 123 SER cc_start: 0.7997 (m) cc_final: 0.7696 (p) REVERT: C 211 LYS cc_start: 0.8489 (mttt) cc_final: 0.8148 (mtpt) REVERT: C 221 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.8076 (t-90) REVERT: C 232 GLU cc_start: 0.7136 (pm20) cc_final: 0.6867 (pt0) REVERT: C 337 GLN cc_start: 0.8223 (tp40) cc_final: 0.7934 (mm-40) REVERT: E 28 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7219 (mt-10) REVERT: E 305 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: E 356 ASP cc_start: 0.8082 (t0) cc_final: 0.7710 (t0) REVERT: E 362 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.6971 (tmm) REVERT: F 123 SER cc_start: 0.7923 (m) cc_final: 0.7619 (p) REVERT: F 211 LYS cc_start: 0.8304 (mttt) cc_final: 0.7991 (mtpt) REVERT: D 356 ASP cc_start: 0.8078 (t0) cc_final: 0.7749 (t0) REVERT: D 403 ARG cc_start: 0.7970 (ttt90) cc_final: 0.7620 (ttt90) REVERT: D 410 GLN cc_start: 0.7948 (mp10) cc_final: 0.7527 (mm-40) outliers start: 45 outliers final: 24 residues processed: 345 average time/residue: 0.8786 time to fit residues: 341.5115 Evaluate side-chains 348 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 319 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain I residue 13 TYR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [156, 174, 140, 21, 76, 4, 99, 165, 58, 14, 146] chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 ASN B 272 GLN A 118 GLN C 112 GLN C 167 ASN E 309 ASN F 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099946 restraints weight = 57199.315| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.11 r_work: 0.3234 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15198 Z= 0.211 Angle : 0.895 25.742 20741 Z= 0.450 Chirality : 0.171 1.735 2494 Planarity : 0.004 0.046 2553 Dihedral : 6.282 59.628 2811 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.79 % Allowed : 19.76 % Favored : 77.45 % Cbeta Deviations : 0.27 % 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: 0.45 (0.20), residues: 1910 helix: 2.93 (0.18), residues: 792 sheet: -0.52 (0.33), residues: 294 loop : -2.22 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 258 TYR 0.015 0.001 TYR B 106 PHE 0.015 0.001 PHE E 393 TRP 0.019 0.001 TRP C 119 HIS 0.004 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (15196) covalent geometry : angle 0.89477 / 0.45 (20735) hydrogen bonds : bond 0.08066 / 5.36 ( 737) hydrogen bonds : angle 4.06393 / 2.98 ( 2109) link_NAG-ASN : bond 0.00157 / 0.08 ( 2) link_NAG-ASN : angle 1.73575 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7798 (mtt) REVERT: A 151 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8150 (ttmm) REVERT: I 13 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.5580 (m-10) REVERT: C 123 SER cc_start: 0.7979 (m) cc_final: 0.7692 (p) REVERT: C 211 LYS cc_start: 0.8478 (mttt) cc_final: 0.8154 (mtpt) REVERT: C 221 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.8114 (t-90) REVERT: C 337 GLN cc_start: 0.8312 (tp40) cc_final: 0.8060 (mm-40) REVERT: E 28 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7221 (mt-10) REVERT: E 305 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: E 356 ASP cc_start: 0.8080 (t0) cc_final: 0.7707 (t0) REVERT: E 362 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.6937 (tmm) REVERT: E 435 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7517 (mtpt) REVERT: F 123 SER cc_start: 0.8008 (m) cc_final: 0.7734 (p) REVERT: F 190 THR cc_start: 0.8767 (m) cc_final: 0.8516 (p) REVERT: F 211 LYS cc_start: 0.8333 (mttt) cc_final: 0.8027 (mtpt) REVERT: D 356 ASP cc_start: 0.8082 (t0) cc_final: 0.7768 (t0) REVERT: D 403 ARG cc_start: 0.7985 (ttt90) cc_final: 0.7644 (ttt90) REVERT: D 410 GLN cc_start: 0.7958 (mp10) cc_final: 0.7513 (mm-40) outliers start: 42 outliers final: 22 residues processed: 339 average time/residue: 0.8752 time to fit residues: 335.1442 Evaluate side-chains 351 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain I residue 13 TYR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [184, 114, 154, 35, 43, 11, 66, 124, 101, 44, 180] chunk 184 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN B 272 GLN A 18 ASN A 118 GLN A 301 ASN C 112 GLN C 167 ASN E 309 ASN F 112 GLN F 167 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099767 restraints weight = 57212.022| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.10 r_work: 0.3230 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15198 Z= 0.215 Angle : 0.897 26.124 20741 Z= 0.451 Chirality : 0.171 1.734 2494 Planarity : 0.004 0.047 2553 Dihedral : 6.223 59.514 2811 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 2.72 % Allowed : 19.89 % Favored : 77.39 % Cbeta Deviations : 0.27 % 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: 0.45 (0.20), residues: 1910 helix: 2.94 (0.18), residues: 792 sheet: -0.48 (0.33), residues: 294 loop : -2.23 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 50 TYR 0.015 0.002 TYR F 267 PHE 0.015 0.001 PHE E 393 TRP 0.019 0.001 TRP C 119 HIS 0.004 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (15196) covalent geometry : angle 0.89613 / 0.45 (20735) hydrogen bonds : bond 0.08110 / 5.39 ( 737) hydrogen bonds : angle 4.05717 / 2.98 ( 2109) link_NAG-ASN : bond 0.00120 / 0.06 ( 2) link_NAG-ASN : angle 1.82655 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 330 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7784 (mtt) REVERT: B 301 ASN cc_start: 0.8415 (m110) cc_final: 0.8135 (m110) REVERT: A 151 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8155 (ttmm) REVERT: I 13 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.5653 (m-10) REVERT: C 123 SER cc_start: 0.7969 (m) cc_final: 0.7688 (p) REVERT: C 211 LYS cc_start: 0.8497 (mttt) cc_final: 0.8192 (mtpt) REVERT: C 221 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.8059 (t-90) REVERT: C 296 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7390 (tpp) REVERT: C 337 GLN cc_start: 0.8289 (tp40) cc_final: 0.8056 (mm-40) REVERT: E 28 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7216 (mt-10) REVERT: E 305 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: E 356 ASP cc_start: 0.8034 (t0) cc_final: 0.7669 (t0) REVERT: E 362 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: E 435 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7526 (mtpt) REVERT: E 469 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8582 (tt) REVERT: F 123 SER cc_start: 0.7938 (m) cc_final: 0.7525 (p) REVERT: F 190 THR cc_start: 0.8772 (m) cc_final: 0.8540 (p) REVERT: F 211 LYS cc_start: 0.8324 (mttt) cc_final: 0.8009 (mtpt) REVERT: F 273 ILE cc_start: 0.8516 (mm) cc_final: 0.8308 (mm) REVERT: D 356 ASP cc_start: 0.8088 (t0) cc_final: 0.7770 (t0) REVERT: D 403 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7629 (ttt90) REVERT: D 410 GLN cc_start: 0.7992 (mp10) cc_final: 0.7530 (mm-40) outliers start: 41 outliers final: 24 residues processed: 346 average time/residue: 0.8803 time to fit residues: 344.7231 Evaluate side-chains 361 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain I residue 13 TYR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [45, 55, 106, 170, 159, 140, 83, 74, 18, 92, 129] chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 170 optimal weight: 0.0270 chunk 159 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN B 32 ASN B 272 GLN A 18 ASN A 118 GLN C 112 GLN E 309 ASN F 112 GLN F 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099331 restraints weight = 56904.159| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.10 r_work: 0.3224 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15198 Z= 0.237 Angle : 0.907 26.010 20741 Z= 0.457 Chirality : 0.171 1.739 2494 Planarity : 0.004 0.047 2553 Dihedral : 6.230 59.740 2811 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 2.92 % Allowed : 20.23 % Favored : 76.86 % Cbeta Deviations : 0.27 % 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 (0.20), residues: 1910 helix: 2.88 (0.18), residues: 792 sheet: -0.50 (0.33), residues: 298 loop : -2.27 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 50 TYR 0.020 0.002 TYR B 106 PHE 0.016 0.002 PHE E 393 TRP 0.020 0.002 TRP F 119 HIS 0.005 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (15196) covalent geometry : angle 0.90609 / 0.46 (20735) hydrogen bonds : bond 0.08405 / 5.59 ( 737) hydrogen bonds : angle 4.10457 / 3.02 ( 2109) link_NAG-ASN : bond 0.00107 / 0.05 ( 2) link_NAG-ASN : angle 1.89488 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 331 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: A 121 SER cc_start: 0.8201 (t) cc_final: 0.7956 (p) REVERT: A 151 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8172 (ttmm) REVERT: I 13 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.5650 (m-10) REVERT: C 123 SER cc_start: 0.7978 (m) cc_final: 0.7698 (p) REVERT: C 211 LYS cc_start: 0.8502 (mttt) cc_final: 0.8204 (mtpt) REVERT: C 221 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.8141 (t-90) REVERT: C 296 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7443 (tpp) REVERT: C 337 GLN cc_start: 0.8324 (tp40) cc_final: 0.8109 (mm-40) REVERT: E 28 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7228 (mt-10) REVERT: E 356 ASP cc_start: 0.8073 (t0) cc_final: 0.7702 (t0) REVERT: E 435 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7554 (mtpt) REVERT: F 123 SER cc_start: 0.7922 (m) cc_final: 0.7543 (p) REVERT: F 190 THR cc_start: 0.8774 (m) cc_final: 0.8539 (p) REVERT: F 211 LYS cc_start: 0.8333 (mttt) cc_final: 0.8018 (mtpt) REVERT: D 356 ASP cc_start: 0.8100 (t0) cc_final: 0.7781 (t0) REVERT: D 403 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7723 (ttt90) REVERT: D 410 GLN cc_start: 0.8037 (mp10) cc_final: 0.7636 (mp10) REVERT: D 435 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7599 (mtpt) outliers start: 44 outliers final: 24 residues processed: 350 average time/residue: 0.8706 time to fit residues: 343.9203 Evaluate side-chains 362 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 13 TYR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [154, 41, 81, 140, 63, 164, 66, 185, 144, 169, 36] chunk 154 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN B 32 ASN B 272 GLN A 18 ASN A 118 GLN C 92 ASN C 112 GLN E 309 ASN F 112 GLN F 167 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098957 restraints weight = 57026.039| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.11 r_work: 0.3219 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15198 Z= 0.254 Angle : 0.917 26.053 20741 Z= 0.463 Chirality : 0.172 1.741 2494 Planarity : 0.004 0.048 2553 Dihedral : 6.169 60.020 2807 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 2.79 % Allowed : 20.23 % Favored : 76.99 % Cbeta Deviations : 0.27 % 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: 0.34 (0.20), residues: 1910 helix: 2.84 (0.18), residues: 792 sheet: -0.49 (0.33), residues: 298 loop : -2.31 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 37 TYR 0.017 0.002 TYR B 106 PHE 0.017 0.002 PHE E 393 TRP 0.021 0.002 TRP F 119 HIS 0.005 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 (15196) covalent geometry : angle 0.91623 / 0.46 (20735) hydrogen bonds : bond 0.08610 / 5.72 ( 737) hydrogen bonds : angle 4.15131 / 3.06 ( 2109) link_NAG-ASN : bond 0.00105 / 0.05 ( 2) link_NAG-ASN : angle 1.88753 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7836 (mtt) REVERT: A 151 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8174 (ttmm) REVERT: I 13 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.5520 (m-10) REVERT: C 123 SER cc_start: 0.8009 (OUTLIER) cc_final: 0.7740 (p) REVERT: C 211 LYS cc_start: 0.8493 (mttt) cc_final: 0.8201 (mtpt) REVERT: C 221 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8121 (t-90) REVERT: C 296 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7423 (tpp) REVERT: C 337 GLN cc_start: 0.8310 (tp40) cc_final: 0.8032 (mm-40) REVERT: E 28 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7236 (mt-10) REVERT: E 356 ASP cc_start: 0.8078 (t0) cc_final: 0.7705 (t0) REVERT: E 435 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7558 (mtpt) REVERT: F 123 SER cc_start: 0.7909 (m) cc_final: 0.7493 (p) REVERT: D 356 ASP cc_start: 0.8067 (t0) cc_final: 0.7750 (t0) REVERT: D 403 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7730 (ttt90) REVERT: D 410 GLN cc_start: 0.8036 (mp10) cc_final: 0.7629 (mp10) REVERT: D 435 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7602 (mtpt) outliers start: 42 outliers final: 24 residues processed: 350 average time/residue: 0.8682 time to fit residues: 342.9283 Evaluate side-chains 359 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 328 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain I residue 13 TYR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [150, 26, 92, 154, 13, 151, 134, 178, 177, 116, 143] chunk 150 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 143 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN B 32 ASN B 272 GLN A 18 ASN A 118 GLN C 112 GLN E 309 ASN F 112 GLN F 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101775 restraints weight = 57160.001| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.11 r_work: 0.3264 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15198 Z= 0.132 Angle : 0.873 26.782 20741 Z= 0.435 Chirality : 0.170 1.721 2494 Planarity : 0.004 0.043 2553 Dihedral : 5.789 58.621 2807 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.72 % Allowed : 21.42 % Favored : 76.86 % Cbeta Deviations : 0.22 % 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: 0.69 (0.20), residues: 1910 helix: 3.21 (0.18), residues: 794 sheet: -0.52 (0.31), residues: 316 loop : -2.17 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 37 TYR 0.017 0.001 TYR F 267 PHE 0.011 0.001 PHE E 393 TRP 0.014 0.001 TRP C 119 HIS 0.003 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15196) covalent geometry : angle 0.87317 / 0.44 (20735) hydrogen bonds : bond 0.06752 / 4.49 ( 737) hydrogen bonds : angle 3.87130 / 2.85 ( 2109) link_NAG-ASN : bond 0.00096 / 0.05 ( 2) link_NAG-ASN : angle 1.64571 / 0.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 359 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 333 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7674 (mtt) REVERT: B 301 ASN cc_start: 0.8378 (m110) cc_final: 0.8068 (m110) REVERT: A 151 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8062 (ttmm) REVERT: C 123 SER cc_start: 0.7856 (m) cc_final: 0.7579 (p) REVERT: C 190 THR cc_start: 0.8719 (m) cc_final: 0.8494 (p) REVERT: C 211 LYS cc_start: 0.8456 (mttt) cc_final: 0.8162 (mtpt) REVERT: C 221 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.8104 (t-90) REVERT: C 337 GLN cc_start: 0.8178 (tp40) cc_final: 0.7936 (mm-40) REVERT: E 28 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7179 (mt-10) REVERT: E 356 ASP cc_start: 0.8021 (t0) cc_final: 0.7635 (t0) REVERT: E 362 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.6862 (tmm) REVERT: E 435 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7502 (mtpt) REVERT: F 123 SER cc_start: 0.7859 (m) cc_final: 0.7420 (p) REVERT: F 190 THR cc_start: 0.8746 (m) cc_final: 0.8508 (p) REVERT: D 356 ASP cc_start: 0.8062 (t0) cc_final: 0.7750 (t0) REVERT: D 403 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7634 (ttt90) REVERT: D 410 GLN cc_start: 0.8019 (mp10) cc_final: 0.7558 (mm-40) outliers start: 26 outliers final: 14 residues processed: 345 average time/residue: 0.8647 time to fit residues: 337.2670 Evaluate side-chains 343 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 325 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [56, 144, 41, 171, 138, 116, 49, 175, 94, 139, 47] chunk 56 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 116 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN B 32 ASN A 18 ASN A 118 GLN C 112 GLN C 167 ASN E 309 ASN F 112 GLN F 167 ASN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102386 restraints weight = 57032.875| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.10 r_work: 0.3272 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15198 Z= 0.134 Angle : 0.872 26.568 20741 Z= 0.433 Chirality : 0.170 1.721 2494 Planarity : 0.004 0.054 2553 Dihedral : 5.614 57.590 2807 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.26 % Allowed : 22.21 % Favored : 76.53 % Cbeta Deviations : 0.27 % 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: 0.83 (0.20), residues: 1910 helix: 3.34 (0.18), residues: 794 sheet: -0.48 (0.31), residues: 316 loop : -2.09 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 398 TYR 0.016 0.001 TYR H 63 PHE 0.010 0.001 PHE A 55 TRP 0.014 0.001 TRP C 119 HIS 0.003 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15196) covalent geometry : angle 0.87191 / 0.43 (20735) hydrogen bonds : bond 0.06426 / 4.28 ( 737) hydrogen bonds : angle 3.75962 / 2.77 ( 2109) link_NAG-ASN : bond 0.00102 / 0.05 ( 2) link_NAG-ASN : angle 1.53213 / 0.87 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue TYR 13 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 202 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 380 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 396 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue MET 400 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 328 time to evaluate : 0.576 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: B 218 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7653 (mtt) REVERT: A 151 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8043 (ttmm) REVERT: C 123 SER cc_start: 0.7857 (m) cc_final: 0.7560 (p) REVERT: C 190 THR cc_start: 0.8725 (m) cc_final: 0.8501 (p) REVERT: C 211 LYS cc_start: 0.8459 (mttt) cc_final: 0.8164 (mtpt) REVERT: C 221 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8054 (t-90) REVERT: C 337 GLN cc_start: 0.8203 (tp40) cc_final: 0.7947 (mm-40) REVERT: E 28 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7164 (mt-10) REVERT: E 356 ASP cc_start: 0.8077 (t0) cc_final: 0.7696 (t0) REVERT: E 435 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7521 (mtpt) REVERT: F 68 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6600 (mpt) REVERT: F 123 SER cc_start: 0.7834 (m) cc_final: 0.7405 (p) REVERT: F 190 THR cc_start: 0.8742 (m) cc_final: 0.8513 (p) REVERT: D 32 GLN cc_start: 0.8388 (tp40) cc_final: 0.8084 (tp40) REVERT: D 356 ASP cc_start: 0.8075 (t0) cc_final: 0.7768 (t0) REVERT: D 403 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7621 (ttt90) REVERT: D 410 GLN cc_start: 0.7995 (mp10) cc_final: 0.7535 (mm-40) outliers start: 19 outliers final: 10 residues processed: 336 average time/residue: 0.8971 time to fit residues: 339.1210 Evaluate side-chains 338 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 324 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [126, 9, 98, 49, 85, 91, 23, 19, 166, 15, 71] chunk 126 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 ASN B 32 ASN B 272 GLN A 18 ASN A 118 GLN C 112 GLN C 167 ASN E 309 ASN F 112 GLN F 167 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101007 restraints weight = 56766.703| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.09 r_work: 0.3249 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15198 Z= 0.175 Angle : 0.885 26.123 20741 Z= 0.442 Chirality : 0.170 1.725 2494 Planarity : 0.004 0.044 2553 Dihedral : 5.652 56.865 2807 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.53 % Allowed : 22.15 % Favored : 76.33 % Cbeta Deviations : 0.27 % 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: 0.74 (0.20), residues: 1910 helix: 3.26 (0.18), residues: 792 sheet: -0.53 (0.32), residues: 306 loop : -2.09 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 258 TYR 0.018 0.001 TYR H 63 PHE 0.012 0.001 PHE E 393 TRP 0.016 0.001 TRP F 119 HIS 0.004 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (15196) covalent geometry : angle 0.88518 / 0.44 (20735) hydrogen bonds : bond 0.07204 / 4.79 ( 737) hydrogen bonds : angle 3.84466 / 2.83 ( 2109) link_NAG-ASN : bond 0.00111 / 0.06 ( 2) link_NAG-ASN : angle 1.64011 / 0.93 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9136.65 seconds wall clock time: 155 minutes 3.97 seconds (9303.97 seconds total)