Starting phenix.real_space_refine on Sun Jul 5 09:14:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3j_25660/07_2026/7t3j_25660.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 60 5.49 5 S 33 5.16 5 C 16843 2.51 5 N 4913 2.21 5 O 5227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27076 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 9, 'ARG:plan': 9, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.88, per 1000 atoms: 0.22 Number of scatterers: 27076 At special positions: 0 Unit cell: (128.1, 161.7, 175.35, 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 33 16.00 P 60 15.00 O 5227 8.00 N 4913 7.00 C 16843 6.00 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 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6226 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 53 sheets defined 34.8% alpha, 20.6% beta 5 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.944A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.128A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.899A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.910A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.506A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.519A pdb=" N ASP A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.774A pdb=" N LEU A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.686A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.728A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.744A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.536A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.902A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.597A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.899A pdb=" N GLY B 312 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.991A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 removed outlier: 3.528A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.730A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.837A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 150 through 163 removed outlier: 3.610A pdb=" N ALA D 154 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.521A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.530A pdb=" N GLY E 305 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 322 through 332 removed outlier: 3.532A pdb=" N LEU E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.796A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 171 removed outlier: 6.331A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.522A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 removed outlier: 3.754A pdb=" N ILE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 147 " --> pdb=" O THR J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.537A pdb=" N VAL J 151 " --> pdb=" O PRO J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 169 Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 191 through 200 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 4.666A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 142 through 147 removed outlier: 3.872A pdb=" N LEU K 146 " --> pdb=" O TRP K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 200 removed outlier: 3.567A pdb=" N PHE K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 5.658A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.221A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.780A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 61 removed outlier: 3.891A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.696A pdb=" N ASN B 220 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.880A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.771A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 307 removed outlier: 3.575A pdb=" N LYS D 312 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.806A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.829A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 63 through 70 removed outlier: 4.513A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.911A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 64 through 70 Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.672A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.899A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 4.377A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.983A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 188 through 196 removed outlier: 6.472A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG H 194 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL H 179 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP H 196 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 177 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 261 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR H 97 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS H 263 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU H 265 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA H 101 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE7, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.944A pdb=" N VAL H 307 " --> pdb=" O LYS H 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.698A pdb=" N GLY I 353 " --> pdb=" O PHE I 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.945A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.575A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR J 12 " --> pdb=" O TYR J 31 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR J 31 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA J 14 " --> pdb=" O THR J 29 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR J 29 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG J 16 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN J 27 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS J 26 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR J 41 " --> pdb=" O HIS J 26 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP J 28 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE J 39 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU J 30 " --> pdb=" O MET J 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF5, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.524A pdb=" N VAL I 307 " --> pdb=" O LYS I 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 85 through 91 removed outlier: 3.603A pdb=" N ASP J 73 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.198A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 85 through 90 removed outlier: 5.362A pdb=" N LEU K 119 " --> pdb=" O THR K 113 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7141 1.33 - 1.45: 5339 1.45 - 1.57: 15125 1.57 - 1.69: 120 1.69 - 1.81: 52 Bond restraints: 27777 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" CB ARG A 302 " pdb=" CG ARG A 302 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.83e+00 bond pdb=" CA LYS A 71 " pdb=" C LYS A 71 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.26e-02 6.30e+03 2.62e+00 bond pdb=" CB GLN K 27 " pdb=" CG GLN K 27 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" C HIS C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.61e+00 ... (remaining 27772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 37388 2.44 - 4.88: 558 4.88 - 7.32: 79 7.32 - 9.76: 18 9.76 - 12.21: 2 Bond angle restraints: 38045 Sorted by residual: angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CB MET K 1 " pdb=" CG MET K 1 " pdb=" SD MET K 1 " ideal model delta sigma weight residual 112.70 124.91 -12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C PRO B 205 " pdb=" N GLU B 206 " pdb=" CA GLU B 206 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" N PRO D 246 " pdb=" CD PRO D 246 " pdb=" CG PRO D 246 " ideal model delta sigma weight residual 103.20 97.50 5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CB PRO D 246 " pdb=" CG PRO D 246 " pdb=" CD PRO D 246 " ideal model delta sigma weight residual 106.10 94.00 12.10 3.20e+00 9.77e-02 1.43e+01 ... (remaining 38040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 16060 35.77 - 71.54: 411 71.54 - 107.31: 27 107.31 - 143.08: 1 143.08 - 178.85: 6 Dihedral angle restraints: 16505 sinusoidal: 6859 harmonic: 9646 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.46 147.54 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 52.68 147.32 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' C M 37 " pdb=" C1' C M 37 " pdb=" N1 C M 37 " pdb=" C2 C M 37 " ideal model delta sinusoidal sigma weight residual 232.00 53.15 178.85 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3696 0.065 - 0.131: 534 0.131 - 0.196: 40 0.196 - 0.261: 7 0.261 - 0.327: 3 Chirality restraints: 4280 Sorted by residual: chirality pdb=" CB ILE E 72 " pdb=" CA ILE E 72 " pdb=" CG1 ILE E 72 " pdb=" CG2 ILE E 72 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE K 6 " pdb=" CA ILE K 6 " pdb=" CG1 ILE K 6 " pdb=" CG2 ILE K 6 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB THR E 97 " pdb=" CA THR E 97 " pdb=" OG1 THR E 97 " pdb=" CG2 THR E 97 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4277 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 82 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO F 83 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A 72 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 162 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO C 163 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 163 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 163 " 0.042 5.00e-02 4.00e+02 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4988 2.77 - 3.30: 24372 3.30 - 3.84: 48736 3.84 - 4.37: 57947 4.37 - 4.90: 96063 Nonbonded interactions: 232106 Sorted by model distance: nonbonded pdb=" OE1 GLN K 27 " pdb=" OG1 THR K 41 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR G 290 " pdb=" O GLY G 297 " model vdw 2.244 3.040 nonbonded pdb=" O ALA J 141 " pdb=" OG1 THR J 144 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B 24 " pdb=" O PHE B 31 " model vdw 2.282 3.040 nonbonded pdb=" O VAL C 100 " pdb=" OG SER C 179 " model vdw 2.298 3.040 ... (remaining 232101 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.850 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.004 0.072 27777 Z= 0.176 Angle : 0.740 12.205 38045 Z= 0.396 Chirality : 0.046 0.327 4280 Planarity : 0.007 0.127 4785 Dihedral : 16.168 178.855 10279 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.58 % Allowed : 17.10 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 3322 helix: -1.34 (0.12), residues: 1056 sheet: 0.44 (0.23), residues: 522 loop : -1.77 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 14 TYR 0.045 0.002 TYR D 304 PHE 0.015 0.002 PHE K 212 TRP 0.020 0.001 TRP E 193 HIS 0.008 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (27777) covalent geometry : angle 0.73956 / 0.40 (38045) hydrogen bonds : bond 0.15379 / 10.24 ( 1107) hydrogen bonds : angle 7.36843 / 5.11 ( 3094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7735 (mpt-90) cc_final: 0.7517 (mmp-170) REVERT: G 51 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: I 203 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.7057 (ttm110) REVERT: J 113 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8950 (p) REVERT: K 62 PHE cc_start: 0.8702 (t80) cc_final: 0.8476 (t80) outliers start: 15 outliers final: 4 residues processed: 245 average time/residue: 0.1670 time to fit residues: 64.9827 Evaluate side-chains 223 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.110139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089729 restraints weight = 64045.768| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.06 r_work: 0.3292 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27777 Z= 0.114 Angle : 0.509 6.915 38045 Z= 0.269 Chirality : 0.039 0.210 4280 Planarity : 0.005 0.076 4785 Dihedral : 11.209 177.798 4400 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.30 % Allowed : 16.26 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3322 helix: 0.24 (0.15), residues: 1057 sheet: 0.72 (0.23), residues: 503 loop : -1.49 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 14 TYR 0.011 0.001 TYR A 187 PHE 0.011 0.001 PHE I 114 TRP 0.011 0.001 TRP A 362 HIS 0.005 0.001 HIS G 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (27777) covalent geometry : angle 0.50923 / 0.27 (38045) hydrogen bonds : bond 0.03809 / 2.55 ( 1107) hydrogen bonds : angle 5.35789 / 3.73 ( 3094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6446 (ttp-170) cc_final: 0.5492 (tpm170) REVERT: B 139 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7415 (tp) REVERT: D 216 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6594 (mt-10) REVERT: I 203 ARG cc_start: 0.7848 (ptp-110) cc_final: 0.7503 (ttm110) outliers start: 34 outliers final: 14 residues processed: 265 average time/residue: 0.1721 time to fit residues: 71.0555 Evaluate side-chains 223 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 320 optimal weight: 5.9990 chunk 268 optimal weight: 0.0870 chunk 254 optimal weight: 0.3980 chunk 252 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 324 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 348 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 ASN J 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.108733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088118 restraints weight = 75588.980| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.21 r_work: 0.3237 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27777 Z= 0.128 Angle : 0.502 6.147 38045 Z= 0.262 Chirality : 0.039 0.196 4280 Planarity : 0.004 0.058 4785 Dihedral : 10.988 177.119 4390 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.11 % Allowed : 15.99 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3322 helix: 0.83 (0.15), residues: 1066 sheet: 0.74 (0.23), residues: 508 loop : -1.34 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.015 0.001 TYR H 290 PHE 0.011 0.001 PHE I 114 TRP 0.013 0.001 TRP K 159 HIS 0.012 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (27777) covalent geometry : angle 0.50192 / 0.26 (38045) hydrogen bonds : bond 0.03429 / 2.28 ( 1107) hydrogen bonds : angle 5.02215 / 3.50 ( 3094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6129 (ttp-170) cc_final: 0.5136 (tpm170) REVERT: B 139 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7463 (tp) REVERT: F 143 THR cc_start: 0.8973 (p) cc_final: 0.8757 (p) REVERT: F 216 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: G 87 ASP cc_start: 0.8457 (m-30) cc_final: 0.8107 (m-30) REVERT: G 94 ASN cc_start: 0.8752 (p0) cc_final: 0.8525 (p0) REVERT: I 203 ARG cc_start: 0.7996 (ptp-110) cc_final: 0.7649 (ttm110) REVERT: K 126 ASN cc_start: 0.7567 (m-40) cc_final: 0.7264 (m110) REVERT: K 197 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8093 (mtmm) outliers start: 55 outliers final: 29 residues processed: 269 average time/residue: 0.1747 time to fit residues: 74.3162 Evaluate side-chains 250 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 305 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 306 optimal weight: 3.9990 chunk 288 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 242 optimal weight: 0.3980 chunk 271 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS G 343 HIS ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN K 26 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.109313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088559 restraints weight = 62908.236| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.06 r_work: 0.3278 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27777 Z= 0.103 Angle : 0.485 8.077 38045 Z= 0.251 Chirality : 0.039 0.328 4280 Planarity : 0.004 0.059 4785 Dihedral : 10.919 176.941 4390 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.07 % Allowed : 16.49 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3322 helix: 1.17 (0.16), residues: 1072 sheet: 0.79 (0.23), residues: 514 loop : -1.26 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 156 TYR 0.013 0.001 TYR H 290 PHE 0.008 0.001 PHE J 195 TRP 0.011 0.001 TRP A 362 HIS 0.013 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (27777) covalent geometry : angle 0.48475 / 0.25 (38045) hydrogen bonds : bond 0.03111 / 2.06 ( 1107) hydrogen bonds : angle 4.80239 / 3.35 ( 3094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6206 (ttp-170) cc_final: 0.5232 (tpm170) REVERT: B 170 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7944 (ptm-80) REVERT: C 46 ASP cc_start: 0.5462 (p0) cc_final: 0.5057 (p0) REVERT: D 44 MET cc_start: 0.6971 (mpp) cc_final: 0.6606 (ptp) REVERT: E 52 ARG cc_start: 0.7086 (mtm180) cc_final: 0.6711 (mtm180) REVERT: E 105 SER cc_start: 0.7177 (m) cc_final: 0.6720 (t) REVERT: F 216 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: F 283 LEU cc_start: 0.8569 (mt) cc_final: 0.8248 (mt) REVERT: G 87 ASP cc_start: 0.8360 (m-30) cc_final: 0.7932 (m-30) REVERT: G 94 ASN cc_start: 0.8673 (p0) cc_final: 0.8443 (p0) REVERT: G 159 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7781 (m-70) REVERT: I 203 ARG cc_start: 0.7905 (ptp-110) cc_final: 0.7564 (ttm110) REVERT: K 57 ASP cc_start: 0.7966 (p0) cc_final: 0.7692 (m-30) REVERT: K 62 PHE cc_start: 0.8751 (t80) cc_final: 0.8525 (t80) REVERT: K 197 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8075 (mtmm) outliers start: 54 outliers final: 29 residues processed: 277 average time/residue: 0.1688 time to fit residues: 74.0290 Evaluate side-chains 251 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 304 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 247 optimal weight: 4.9990 chunk 300 optimal weight: 0.7980 chunk 219 optimal weight: 0.3980 chunk 152 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 315 optimal weight: 0.0670 chunk 207 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS H 343 HIS I 186 GLN I 260 GLN J 194 ASN K 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.109509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089101 restraints weight = 66059.138| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.93 r_work: 0.3286 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27777 Z= 0.099 Angle : 0.481 6.666 38045 Z= 0.249 Chirality : 0.038 0.308 4280 Planarity : 0.004 0.058 4785 Dihedral : 10.868 178.075 4390 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.96 % Allowed : 16.53 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3322 helix: 1.39 (0.16), residues: 1066 sheet: 0.79 (0.23), residues: 515 loop : -1.22 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 156 TYR 0.013 0.001 TYR H 290 PHE 0.009 0.001 PHE J 195 TRP 0.010 0.001 TRP A 362 HIS 0.012 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (27777) covalent geometry : angle 0.48122 / 0.25 (38045) hydrogen bonds : bond 0.03041 / 2.02 ( 1107) hydrogen bonds : angle 4.68072 / 3.27 ( 3094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6078 (ttp-170) cc_final: 0.5100 (tpm170) REVERT: A 121 LEU cc_start: 0.7035 (mt) cc_final: 0.6718 (mt) REVERT: A 366 LEU cc_start: 0.7235 (tp) cc_final: 0.6977 (tp) REVERT: B 170 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8040 (ptm-80) REVERT: C 46 ASP cc_start: 0.5483 (p0) cc_final: 0.5146 (p0) REVERT: D 44 MET cc_start: 0.6934 (mpp) cc_final: 0.6660 (ptp) REVERT: E 52 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6757 (mtm180) REVERT: F 143 THR cc_start: 0.9023 (p) cc_final: 0.8778 (p) REVERT: F 216 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: F 283 LEU cc_start: 0.8508 (mt) cc_final: 0.8189 (mt) REVERT: G 87 ASP cc_start: 0.8365 (m-30) cc_final: 0.7944 (m-30) REVERT: G 94 ASN cc_start: 0.8570 (p0) cc_final: 0.8333 (p0) REVERT: I 203 ARG cc_start: 0.7910 (ptp-110) cc_final: 0.7588 (ttm110) REVERT: K 57 ASP cc_start: 0.7884 (p0) cc_final: 0.7614 (m-30) REVERT: K 62 PHE cc_start: 0.8747 (t80) cc_final: 0.8543 (t80) REVERT: K 197 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8054 (mtmm) outliers start: 51 outliers final: 36 residues processed: 268 average time/residue: 0.1756 time to fit residues: 73.7886 Evaluate side-chains 249 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 53 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 275 optimal weight: 0.0770 chunk 224 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS I 186 GLN J 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084965 restraints weight = 62914.968| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.05 r_work: 0.3204 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27777 Z= 0.174 Angle : 0.547 10.392 38045 Z= 0.282 Chirality : 0.041 0.301 4280 Planarity : 0.004 0.057 4785 Dihedral : 10.947 176.020 4390 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.61 % Allowed : 16.53 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3322 helix: 1.30 (0.16), residues: 1065 sheet: 0.58 (0.23), residues: 524 loop : -1.21 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 35 TYR 0.018 0.002 TYR F 290 PHE 0.013 0.001 PHE G 114 TRP 0.013 0.001 TRP E 49 HIS 0.013 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (27777) covalent geometry : angle 0.54747 / 0.28 (38045) hydrogen bonds : bond 0.03406 / 2.24 ( 1107) hydrogen bonds : angle 4.82400 / 3.37 ( 3094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6308 (ttp-170) cc_final: 0.6003 (ttp-170) REVERT: A 121 LEU cc_start: 0.7134 (mt) cc_final: 0.6803 (mt) REVERT: A 228 TRP cc_start: 0.8531 (t-100) cc_final: 0.8314 (t-100) REVERT: A 366 LEU cc_start: 0.7275 (tp) cc_final: 0.7021 (tp) REVERT: B 170 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8078 (ptm-80) REVERT: C 46 ASP cc_start: 0.5545 (p0) cc_final: 0.5178 (p0) REVERT: E 52 ARG cc_start: 0.7153 (mtm180) cc_final: 0.6854 (mtm180) REVERT: E 69 ARG cc_start: 0.7242 (ptt180) cc_final: 0.6953 (tmm-80) REVERT: E 105 SER cc_start: 0.7546 (m) cc_final: 0.6945 (t) REVERT: E 212 ASP cc_start: 0.7490 (m-30) cc_final: 0.7254 (m-30) REVERT: F 216 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: F 283 LEU cc_start: 0.8616 (mt) cc_final: 0.8302 (mt) REVERT: G 87 ASP cc_start: 0.8393 (m-30) cc_final: 0.8021 (m-30) REVERT: G 94 ASN cc_start: 0.8570 (p0) cc_final: 0.8352 (p0) REVERT: K 62 PHE cc_start: 0.8763 (t80) cc_final: 0.8557 (t80) REVERT: K 197 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8068 (mtmm) outliers start: 68 outliers final: 43 residues processed: 280 average time/residue: 0.1778 time to fit residues: 77.4341 Evaluate side-chains 254 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 309 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 322 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 254 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS I 186 GLN J 194 ASN K 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083739 restraints weight = 75496.307| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.14 r_work: 0.3163 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27777 Z= 0.201 Angle : 0.573 8.877 38045 Z= 0.296 Chirality : 0.041 0.262 4280 Planarity : 0.005 0.074 4785 Dihedral : 11.020 176.626 4390 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.03 % Allowed : 17.56 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3322 helix: 1.22 (0.16), residues: 1059 sheet: 0.56 (0.23), residues: 529 loop : -1.21 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.018 0.002 TYR E 290 PHE 0.012 0.002 PHE I 114 TRP 0.014 0.001 TRP I 49 HIS 0.012 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (27777) covalent geometry : angle 0.57274 / 0.30 (38045) hydrogen bonds : bond 0.03543 / 2.33 ( 1107) hydrogen bonds : angle 4.91065 / 3.43 ( 3094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6999 (t80) REVERT: A 58 ARG cc_start: 0.6336 (ttp-170) cc_final: 0.6061 (ttp-170) REVERT: A 120 PHE cc_start: 0.7686 (t80) cc_final: 0.7350 (t80) REVERT: A 121 LEU cc_start: 0.7176 (mt) cc_final: 0.6869 (mt) REVERT: A 228 TRP cc_start: 0.8532 (t-100) cc_final: 0.8304 (t-100) REVERT: A 281 MET cc_start: 0.5807 (mmm) cc_final: 0.5313 (tpt) REVERT: A 366 LEU cc_start: 0.7333 (tp) cc_final: 0.7083 (tp) REVERT: B 170 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8114 (ptm-80) REVERT: C 46 ASP cc_start: 0.5535 (p0) cc_final: 0.5227 (p0) REVERT: D 44 MET cc_start: 0.6905 (mpp) cc_final: 0.6361 (ptp) REVERT: E 69 ARG cc_start: 0.7396 (ptt180) cc_final: 0.7134 (tmm-80) REVERT: F 216 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: G 51 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8334 (mp10) REVERT: G 87 ASP cc_start: 0.8503 (m-30) cc_final: 0.8101 (m-30) REVERT: G 94 ASN cc_start: 0.8558 (p0) cc_final: 0.8349 (p0) REVERT: K 57 ASP cc_start: 0.7991 (p0) cc_final: 0.7659 (m-30) outliers start: 53 outliers final: 45 residues processed: 257 average time/residue: 0.1714 time to fit residues: 68.7344 Evaluate side-chains 249 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 112 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 153 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 0.0050 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN F 160 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 GLN J 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.108033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086915 restraints weight = 72424.960| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.05 r_work: 0.3238 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27777 Z= 0.101 Angle : 0.508 10.325 38045 Z= 0.262 Chirality : 0.039 0.239 4280 Planarity : 0.004 0.057 4785 Dihedral : 10.919 178.162 4390 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.96 % Allowed : 17.87 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3322 helix: 1.51 (0.16), residues: 1059 sheet: 0.66 (0.23), residues: 527 loop : -1.17 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.015 0.001 TYR D 304 PHE 0.009 0.001 PHE J 195 TRP 0.012 0.001 TRP E 193 HIS 0.015 0.001 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (27777) covalent geometry : angle 0.50753 / 0.26 (38045) hydrogen bonds : bond 0.03113 / 2.06 ( 1107) hydrogen bonds : angle 4.66094 / 3.25 ( 3094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6337 (ttp-170) cc_final: 0.6129 (ttp-170) REVERT: A 120 PHE cc_start: 0.7641 (t80) cc_final: 0.7331 (t80) REVERT: A 121 LEU cc_start: 0.7249 (mt) cc_final: 0.6924 (mt) REVERT: A 228 TRP cc_start: 0.8523 (t-100) cc_final: 0.8301 (t-100) REVERT: A 366 LEU cc_start: 0.7402 (tp) cc_final: 0.7151 (tp) REVERT: B 170 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8063 (ptm-80) REVERT: C 46 ASP cc_start: 0.5184 (p0) cc_final: 0.4789 (p0) REVERT: D 44 MET cc_start: 0.6836 (mpp) cc_final: 0.6284 (ptp) REVERT: E 69 ARG cc_start: 0.7225 (ptt180) cc_final: 0.6932 (tmm-80) REVERT: E 105 SER cc_start: 0.7530 (m) cc_final: 0.6955 (t) REVERT: F 216 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: G 51 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: G 87 ASP cc_start: 0.8439 (m-30) cc_final: 0.7986 (m-30) REVERT: G 94 ASN cc_start: 0.8544 (p0) cc_final: 0.8323 (p0) REVERT: I 138 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8675 (mm) REVERT: K 126 ASN cc_start: 0.7487 (m-40) cc_final: 0.7281 (m110) outliers start: 51 outliers final: 38 residues processed: 254 average time/residue: 0.1703 time to fit residues: 68.2613 Evaluate side-chains 242 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 73 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 155 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 0.0570 chunk 253 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN F 160 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN K 26 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.106231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084944 restraints weight = 72519.262| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.03 r_work: 0.3195 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27777 Z= 0.168 Angle : 0.544 11.011 38045 Z= 0.279 Chirality : 0.041 0.274 4280 Planarity : 0.004 0.056 4785 Dihedral : 10.937 176.136 4390 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.99 % Allowed : 17.91 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3322 helix: 1.42 (0.16), residues: 1060 sheet: 0.61 (0.23), residues: 529 loop : -1.18 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.015 0.002 TYR F 290 PHE 0.011 0.001 PHE G 114 TRP 0.013 0.001 TRP E 193 HIS 0.014 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (27777) covalent geometry : angle 0.54380 / 0.28 (38045) hydrogen bonds : bond 0.03332 / 2.19 ( 1107) hydrogen bonds : angle 4.75410 / 3.31 ( 3094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 120 PHE cc_start: 0.7685 (t80) cc_final: 0.7291 (t80) REVERT: A 121 LEU cc_start: 0.7270 (mt) cc_final: 0.6978 (mt) REVERT: A 366 LEU cc_start: 0.7249 (tp) cc_final: 0.7011 (tp) REVERT: B 170 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8096 (ptm-80) REVERT: C 21 MET cc_start: 0.7460 (tpp) cc_final: 0.7221 (tpp) REVERT: C 46 ASP cc_start: 0.5148 (p0) cc_final: 0.4694 (p0) REVERT: D 44 MET cc_start: 0.6910 (mpp) cc_final: 0.6541 (ptp) REVERT: D 302 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7270 (mm-30) REVERT: E 69 ARG cc_start: 0.7203 (ptt180) cc_final: 0.6942 (tmm-80) REVERT: E 193 TRP cc_start: 0.7726 (m-10) cc_final: 0.7369 (m-90) REVERT: F 216 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: G 51 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: G 87 ASP cc_start: 0.8456 (m-30) cc_final: 0.8074 (m-30) REVERT: G 94 ASN cc_start: 0.8563 (p0) cc_final: 0.8351 (p0) REVERT: I 138 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8708 (mm) outliers start: 52 outliers final: 40 residues processed: 249 average time/residue: 0.1695 time to fit residues: 67.3681 Evaluate side-chains 244 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 73 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN K 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.105960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084581 restraints weight = 72371.857| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.11 r_work: 0.3186 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27777 Z= 0.172 Angle : 0.552 10.560 38045 Z= 0.284 Chirality : 0.041 0.297 4280 Planarity : 0.004 0.057 4785 Dihedral : 10.974 176.471 4390 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.88 % Allowed : 18.06 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3322 helix: 1.36 (0.16), residues: 1063 sheet: 0.58 (0.23), residues: 529 loop : -1.22 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.017 0.002 TYR D 304 PHE 0.011 0.001 PHE G 114 TRP 0.017 0.001 TRP A 228 HIS 0.013 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (27777) covalent geometry : angle 0.55167 / 0.28 (38045) hydrogen bonds : bond 0.03395 / 2.22 ( 1107) hydrogen bonds : angle 4.78954 / 3.34 ( 3094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6983 (t80) REVERT: A 120 PHE cc_start: 0.7696 (t80) cc_final: 0.7294 (t80) REVERT: A 121 LEU cc_start: 0.7340 (mt) cc_final: 0.7040 (mt) REVERT: A 366 LEU cc_start: 0.7316 (tp) cc_final: 0.7112 (tp) REVERT: B 170 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8086 (ptm-80) REVERT: C 21 MET cc_start: 0.7461 (tpp) cc_final: 0.7153 (tpp) REVERT: C 46 ASP cc_start: 0.5228 (p0) cc_final: 0.4755 (p0) REVERT: D 44 MET cc_start: 0.6900 (mpp) cc_final: 0.6535 (ptp) REVERT: D 302 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7333 (mm-30) REVERT: E 69 ARG cc_start: 0.7230 (ptt180) cc_final: 0.6962 (tmm-80) REVERT: E 193 TRP cc_start: 0.7693 (m-10) cc_final: 0.7353 (m-90) REVERT: F 64 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (ptm-80) REVERT: F 216 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: G 51 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: G 87 ASP cc_start: 0.8456 (m-30) cc_final: 0.8062 (m-30) REVERT: G 94 ASN cc_start: 0.8536 (p0) cc_final: 0.8327 (p0) outliers start: 49 outliers final: 43 residues processed: 246 average time/residue: 0.1761 time to fit residues: 68.2925 Evaluate side-chains 245 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 73 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 304 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 327 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084794 restraints weight = 65675.655| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.07 r_work: 0.3193 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27777 Z= 0.171 Angle : 0.552 10.705 38045 Z= 0.284 Chirality : 0.041 0.300 4280 Planarity : 0.004 0.056 4785 Dihedral : 10.974 176.487 4390 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.84 % Allowed : 18.06 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3322 helix: 1.35 (0.16), residues: 1064 sheet: 0.52 (0.23), residues: 539 loop : -1.22 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.017 0.002 TYR D 304 PHE 0.010 0.001 PHE J 195 TRP 0.013 0.001 TRP K 159 HIS 0.014 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (27777) covalent geometry : angle 0.55214 / 0.28 (38045) hydrogen bonds : bond 0.03382 / 2.21 ( 1107) hydrogen bonds : angle 4.79489 / 3.34 ( 3094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7142.55 seconds wall clock time: 138 minutes 40.19 seconds (8320.19 seconds total)