Starting phenix.real_space_refine on Fri Sep 27 19:51:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/09_2024/7qh2_13960.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/09_2024/7qh2_13960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/09_2024/7qh2_13960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/09_2024/7qh2_13960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/09_2024/7qh2_13960.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/09_2024/7qh2_13960.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 12 5.49 5 S 98 5.16 5 C 10676 2.51 5 N 2755 2.21 5 O 3265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16808 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 320} Chain: "B" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2041 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 3603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} Conformer: "B" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} bond proxies already assigned to first conformer: 3643 Chain: "D" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 320} Chain: "E" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2041 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' FE': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' FE': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 42 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 42 " occ=0.50 Time building chain proxies: 12.03, per 1000 atoms: 0.72 Number of scatterers: 16808 At special positions: 0 Unit cell: (162.75, 78.12, 115.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 98 16.00 P 12 15.00 O 3265 8.00 N 2755 7.00 C 10676 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: 4.29 Conformation dependent library (CDL) restraints added in 2.7 seconds 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 22 sheets defined 39.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 87 through 104 removed outlier: 3.678A pdb=" N GLU A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.520A pdb=" N ALA A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.546A pdb=" N ARG A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.514A pdb=" N ILE A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.705A pdb=" N GLN A 324 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 380 through 398 Proline residue: A 386 - end of helix removed outlier: 3.525A pdb=" N GLU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Proline residue: A 395 - end of helix Processing helix chain 'B' and resid 36 through 54 removed outlier: 3.726A pdb=" N PHE B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.778A pdb=" N LEU B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.711A pdb=" N GLY B 91 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 128 through 138 removed outlier: 3.556A pdb=" N GLU B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 4.069A pdb=" N ALA B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.655A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 27 through 29 No H-bonds generated for 'chain 'C' and resid 27 through 29' Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.518A pdb=" N PHE C 33 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 35 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.530A pdb=" N LYS C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.691A pdb=" N ALA C 157 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL C 158 " --> pdb=" O MET C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 232 through 239 removed outlier: 3.681A pdb=" N ILE C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.755A pdb=" N PHE C 263 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 3.590A pdb=" N THR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.747A pdb=" N SER C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 353 through 369 Processing helix chain 'C' and resid 393 through 415 Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 438 through 453 Processing helix chain 'D' and resid 87 through 104 removed outlier: 3.679A pdb=" N GLU D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 143 through 159 Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.519A pdb=" N ALA D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Proline residue: D 176 - end of helix removed outlier: 3.546A pdb=" N ARG D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 292 through 301 removed outlier: 3.513A pdb=" N ILE D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 320 through 324 removed outlier: 3.706A pdb=" N GLN D 324 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 380 through 398 Proline residue: D 386 - end of helix removed outlier: 3.525A pdb=" N GLU D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Proline residue: D 395 - end of helix Processing helix chain 'E' and resid 36 through 54 removed outlier: 3.726A pdb=" N PHE E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 67 through 78 removed outlier: 3.777A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.712A pdb=" N GLY E 91 " --> pdb=" O ARG E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 109 Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.556A pdb=" N GLU E 135 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 195 Processing helix chain 'E' and resid 247 through 261 removed outlier: 4.069A pdb=" N ALA E 251 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 removed outlier: 3.704A pdb=" N LEU F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 35 removed outlier: 3.934A pdb=" N HIS F 35 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.726A pdb=" N ASN F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 151 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.710A pdb=" N ALA F 157 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL F 158 " --> pdb=" O MET F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 158' Processing helix chain 'F' and resid 162 through 165 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.661A pdb=" N ILE F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 245 Processing helix chain 'F' and resid 258 through 269 removed outlier: 3.663A pdb=" N PHE F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 305 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 317 through 330 removed outlier: 4.531A pdb=" N ALA F 327 " --> pdb=" O SER F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 removed outlier: 3.634A pdb=" N THR F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 353 through 369 Processing helix chain 'F' and resid 393 through 415 Processing helix chain 'F' and resid 429 through 437 Processing helix chain 'F' and resid 438 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.007A pdb=" N PHE A 225 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA A 188 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR A 227 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR A 75 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY A 166 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N TYR A 77 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 107 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE A 132 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA A 109 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR A 134 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 111 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 131 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.564A pdb=" N GLN A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 195 removed outlier: 5.385A pdb=" N LEU A 201 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR A 218 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET A 213 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE B 231 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN A 215 " --> pdb=" O GLU B 229 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 217 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 227 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 267 removed outlier: 6.067A pdb=" N VAL A 262 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG B 170 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 264 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR B 157 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 147 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 161 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 145 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 176 " --> pdb=" O HIS B 141 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR B 143 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR B 178 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 115 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 179 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS B 117 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 3 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE B 116 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 5 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE B 4 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 60 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 6 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 82 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 309 removed outlier: 7.010A pdb=" N THR A 279 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA A 308 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 281 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 280 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU A 340 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 282 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 358 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET A 377 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 360 " --> pdb=" O MET A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 removed outlier: 4.191A pdb=" N GLU B 18 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.192A pdb=" N THR C 171 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA C 212 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY C 169 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 214 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 167 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 315 removed outlier: 3.630A pdb=" N ALA C 279 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 252 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY C 376 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU C 257 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N SER C 374 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 190 removed outlier: 6.949A pdb=" N PHE D 225 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA D 188 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR D 227 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE D 163 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL D 228 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D 165 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 75 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLY D 166 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N TYR D 77 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 107 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE D 132 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 109 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR D 134 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 111 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL D 131 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.564A pdb=" N GLN D 84 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 192 through 195 removed outlier: 5.383A pdb=" N LEU D 201 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR D 218 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET D 213 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE E 231 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN D 215 " --> pdb=" O GLU E 229 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 217 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN E 227 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 261 through 267 removed outlier: 5.862A pdb=" N VAL D 262 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG E 170 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 264 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR E 157 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS E 147 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN E 161 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL E 145 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU E 176 " --> pdb=" O HIS E 141 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR E 143 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR E 178 " --> pdb=" O THR E 143 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE E 115 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL E 179 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS E 117 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 3 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE E 116 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU E 5 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE E 4 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU E 60 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 6 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY E 82 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 306 through 309 removed outlier: 7.012A pdb=" N THR D 279 " --> pdb=" O THR D 306 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA D 308 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 281 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE D 280 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU D 340 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 282 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE D 358 " --> pdb=" O CYS D 375 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET D 377 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA D 360 " --> pdb=" O MET D 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 19 removed outlier: 3.988A pdb=" N GLU E 18 " --> pdb=" O ILE E 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 23 through 25 Processing sheet with id=AC2, first strand: chain 'F' and resid 101 through 105 removed outlier: 6.185A pdb=" N THR F 171 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA F 212 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY F 169 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU F 214 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL F 167 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'F' and resid 313 through 315 removed outlier: 3.630A pdb=" N ALA F 279 " --> pdb=" O PHE F 230 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 252 " --> pdb=" O THR F 284 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY F 376 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLU F 257 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N SER F 374 " --> pdb=" O GLU F 257 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.12 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2887 1.28 - 1.42: 3865 1.42 - 1.55: 10159 1.55 - 1.68: 38 1.68 - 1.82: 165 Bond restraints: 17114 Sorted by residual: bond pdb=" N PRO E 201 " pdb=" CA PRO E 201 " ideal model delta sigma weight residual 1.469 1.699 -0.230 1.28e-02 6.10e+03 3.23e+02 bond pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 1.467 1.674 -0.207 1.21e-02 6.83e+03 2.92e+02 bond pdb=" C ASN F 459 " pdb=" N PRO F 460 " ideal model delta sigma weight residual 1.332 1.435 -0.103 1.30e-02 5.92e+03 6.30e+01 bond pdb=" C2 FAD C 501 " pdb=" N3 FAD C 501 " ideal model delta sigma weight residual 1.399 1.259 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C2 FAD F 501 " pdb=" N3 FAD F 501 " ideal model delta sigma weight residual 1.399 1.260 0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 17109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 23052 4.29 - 8.59: 145 8.59 - 12.88: 13 12.88 - 17.17: 5 17.17 - 21.47: 1 Bond angle restraints: 23216 Sorted by residual: angle pdb=" C ASN E 200 " pdb=" N PRO E 201 " pdb=" CA PRO E 201 " ideal model delta sigma weight residual 119.84 141.31 -21.47 1.25e+00 6.40e-01 2.95e+02 angle pdb=" C ASN F 459 " pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 119.76 136.90 -17.14 1.03e+00 9.43e-01 2.77e+02 angle pdb=" O CYS C 464 " pdb=" C CYS C 464 " pdb=" N GLN C 465 " ideal model delta sigma weight residual 121.89 105.44 16.45 1.55e+00 4.16e-01 1.13e+02 angle pdb=" CA PRO E 201 " pdb=" N PRO E 201 " pdb=" CD PRO E 201 " ideal model delta sigma weight residual 112.00 97.90 14.10 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N SER E 198 " pdb=" CA SER E 198 " pdb=" C SER E 198 " ideal model delta sigma weight residual 113.18 102.12 11.06 1.33e+00 5.65e-01 6.92e+01 ... (remaining 23211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 10107 31.70 - 63.40: 367 63.40 - 95.10: 42 95.10 - 126.80: 0 126.80 - 158.50: 4 Dihedral angle restraints: 10520 sinusoidal: 4384 harmonic: 6136 Sorted by residual: dihedral pdb=" CA ILE E 197 " pdb=" C ILE E 197 " pdb=" N SER E 198 " pdb=" CA SER E 198 " ideal model delta harmonic sigma weight residual 180.00 145.48 34.52 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA SER E 198 " pdb=" C SER E 198 " pdb=" N LYS E 199 " pdb=" CA LYS E 199 " ideal model delta harmonic sigma weight residual 180.00 148.92 31.08 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N THR E 23 " pdb=" CA THR E 23 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 10517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2283 0.081 - 0.163: 375 0.163 - 0.244: 22 0.244 - 0.326: 4 0.326 - 0.407: 1 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CA PRO F 460 " pdb=" N PRO F 460 " pdb=" C PRO F 460 " pdb=" CB PRO F 460 " both_signs ideal model delta sigma weight residual False 2.72 3.13 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA ILE E 27 " pdb=" N ILE E 27 " pdb=" C ILE E 27 " pdb=" CB ILE E 27 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ARG C 351 " pdb=" N ARG C 351 " pdb=" C ARG C 351 " pdb=" CB ARG C 351 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2682 not shown) Planarity restraints: 2921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 464 " -0.083 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" C CYS C 464 " 0.263 2.00e-02 2.50e+03 pdb=" O CYS C 464 " -0.094 2.00e-02 2.50e+03 pdb=" N GLN C 465 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 501 " 0.010 2.00e-02 2.50e+03 2.06e-02 2.02e+01 pdb=" C10 FAD C 501 " -0.011 2.00e-02 2.50e+03 pdb=" C2 FAD C 501 " 0.028 2.00e-02 2.50e+03 pdb=" C4 FAD C 501 " -0.013 2.00e-02 2.50e+03 pdb=" C4X FAD C 501 " -0.009 2.00e-02 2.50e+03 pdb=" C5X FAD C 501 " -0.003 2.00e-02 2.50e+03 pdb=" C6 FAD C 501 " -0.001 2.00e-02 2.50e+03 pdb=" C7 FAD C 501 " 0.027 2.00e-02 2.50e+03 pdb=" C7M FAD C 501 " 0.038 2.00e-02 2.50e+03 pdb=" C8 FAD C 501 " -0.012 2.00e-02 2.50e+03 pdb=" C8M FAD C 501 " 0.011 2.00e-02 2.50e+03 pdb=" C9 FAD C 501 " -0.019 2.00e-02 2.50e+03 pdb=" C9A FAD C 501 " -0.021 2.00e-02 2.50e+03 pdb=" N1 FAD C 501 " -0.002 2.00e-02 2.50e+03 pdb=" N10 FAD C 501 " -0.034 2.00e-02 2.50e+03 pdb=" N3 FAD C 501 " 0.003 2.00e-02 2.50e+03 pdb=" N5 FAD C 501 " -0.024 2.00e-02 2.50e+03 pdb=" O2 FAD C 501 " 0.041 2.00e-02 2.50e+03 pdb=" O4 FAD C 501 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD F 501 " -0.010 2.00e-02 2.50e+03 2.06e-02 2.02e+01 pdb=" C10 FAD F 501 " 0.011 2.00e-02 2.50e+03 pdb=" C2 FAD F 501 " -0.029 2.00e-02 2.50e+03 pdb=" C4 FAD F 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4X FAD F 501 " 0.009 2.00e-02 2.50e+03 pdb=" C5X FAD F 501 " 0.003 2.00e-02 2.50e+03 pdb=" C6 FAD F 501 " 0.001 2.00e-02 2.50e+03 pdb=" C7 FAD F 501 " -0.027 2.00e-02 2.50e+03 pdb=" C7M FAD F 501 " -0.038 2.00e-02 2.50e+03 pdb=" C8 FAD F 501 " 0.012 2.00e-02 2.50e+03 pdb=" C8M FAD F 501 " -0.011 2.00e-02 2.50e+03 pdb=" C9 FAD F 501 " 0.019 2.00e-02 2.50e+03 pdb=" C9A FAD F 501 " 0.022 2.00e-02 2.50e+03 pdb=" N1 FAD F 501 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FAD F 501 " 0.035 2.00e-02 2.50e+03 pdb=" N3 FAD F 501 " -0.003 2.00e-02 2.50e+03 pdb=" N5 FAD F 501 " 0.024 2.00e-02 2.50e+03 pdb=" O2 FAD F 501 " -0.041 2.00e-02 2.50e+03 pdb=" O4 FAD F 501 " 0.007 2.00e-02 2.50e+03 ... (remaining 2918 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 29 2.32 - 2.96: 7337 2.96 - 3.61: 23840 3.61 - 4.25: 42552 4.25 - 4.90: 68561 Nonbonded interactions: 142319 Sorted by model distance: nonbonded pdb=" OE2 GLU C 422 " pdb="FE FE C 502 " model vdw 1.674 2.260 nonbonded pdb=" OE2 GLU F 422 " pdb="FE FE F 502 " model vdw 1.704 2.260 nonbonded pdb=" NE2 HIS C 377 " pdb="FE FE C 502 " model vdw 1.730 2.340 nonbonded pdb="FE FE C 502 " pdb=" O HOH C 601 " model vdw 1.775 2.260 nonbonded pdb="FE FE F 502 " pdb=" O HOH F 601 " model vdw 1.866 2.260 ... (remaining 142314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 1 through 41 or resid 43 through 467 or resid 501 through \ 502)) selection = (chain 'F' and (resid 1 through 41 or resid 43 through 467 or resid 501 through \ 502)) } 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=0.50 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 43.190 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.008 0.230 17114 Z= 0.483 Angle : 1.008 21.466 23216 Z= 0.599 Chirality : 0.057 0.407 2685 Planarity : 0.008 0.152 2921 Dihedral : 16.285 158.496 6586 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.34 % Favored : 96.43 % Rotamer: Outliers : 2.88 % Allowed : 4.27 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.14), residues: 2129 helix: -4.40 (0.07), residues: 694 sheet: -1.53 (0.21), residues: 430 loop : -1.91 (0.16), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 397 HIS 0.007 0.001 HIS C 441 PHE 0.016 0.002 PHE C 272 TYR 0.029 0.001 TYR C 297 ARG 0.009 0.001 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 2.147 Fit side-chains REVERT: A 84 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8224 (pp30) REVERT: A 126 TYR cc_start: 0.8935 (m-80) cc_final: 0.8407 (m-80) REVERT: A 199 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7991 (m) REVERT: A 226 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7500 (t) REVERT: B 3 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7533 (mmmt) REVERT: B 199 LYS cc_start: 0.4114 (OUTLIER) cc_final: 0.3104 (mmmt) REVERT: C 292 GLN cc_start: 0.8717 (tt0) cc_final: 0.8388 (tt0) REVERT: C 322 ASP cc_start: 0.7703 (m-30) cc_final: 0.7413 (m-30) REVERT: C 366 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8686 (mtmt) REVERT: D 126 TYR cc_start: 0.8964 (m-80) cc_final: 0.8535 (m-80) REVERT: D 226 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7791 (t) REVERT: E 3 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7300 (mmmt) REVERT: E 202 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6342 (pp20) REVERT: E 216 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: F 266 ASP cc_start: 0.8179 (t70) cc_final: 0.7866 (t0) REVERT: F 322 ASP cc_start: 0.7930 (m-30) cc_final: 0.7639 (m-30) REVERT: F 366 LYS cc_start: 0.8726 (mttp) cc_final: 0.8425 (mttt) outliers start: 52 outliers final: 17 residues processed: 231 average time/residue: 1.4751 time to fit residues: 374.0153 Evaluate side-chains 154 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 248 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 107 optimal weight: 0.0470 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 353 GLN A 354 ASN B 16 ASN B 200 ASN C 382 ASN D 115 ASN D 324 GLN D 354 ASN F 292 GLN F 382 ASN F 394 GLN F 423 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17114 Z= 0.174 Angle : 0.577 8.461 23216 Z= 0.303 Chirality : 0.046 0.291 2685 Planarity : 0.006 0.073 2921 Dihedral : 13.953 179.492 2616 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.12 % Favored : 97.65 % Rotamer: Outliers : 1.94 % Allowed : 8.64 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2129 helix: -1.74 (0.16), residues: 720 sheet: -1.17 (0.22), residues: 436 loop : -1.22 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 325 HIS 0.007 0.001 HIS C 441 PHE 0.010 0.001 PHE F 272 TYR 0.022 0.001 TYR C 297 ARG 0.012 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.983 Fit side-chains REVERT: B 227 GLN cc_start: 0.8589 (pm20) cc_final: 0.8350 (pm20) REVERT: B 248 LYS cc_start: 0.8770 (pptt) cc_final: 0.8377 (ptpt) REVERT: C 222 MET cc_start: 0.7897 (mtp) cc_final: 0.7614 (ptp) REVERT: C 258 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7743 (tpp80) REVERT: C 292 GLN cc_start: 0.8469 (tt0) cc_final: 0.8206 (tt0) REVERT: C 322 ASP cc_start: 0.7802 (m-30) cc_final: 0.7546 (m-30) REVERT: C 342 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8591 (ptm) REVERT: D 126 TYR cc_start: 0.8851 (m-80) cc_final: 0.8389 (m-80) REVERT: E 248 LYS cc_start: 0.8714 (pptt) cc_final: 0.8378 (ptpt) REVERT: F 94 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: F 181 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: F 222 MET cc_start: 0.8160 (mmm) cc_final: 0.7369 (mpp) REVERT: F 256 MET cc_start: 0.9044 (ptm) cc_final: 0.8769 (ptp) REVERT: F 342 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8544 (ptm) REVERT: F 369 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8167 (t0) REVERT: F 450 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7913 (tt0) outliers start: 35 outliers final: 14 residues processed: 165 average time/residue: 1.4897 time to fit residues: 271.5841 Evaluate side-chains 147 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 0.0030 chunk 158 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 0.0470 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.5892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 215 ASN D 115 ASN D 353 GLN F 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17114 Z= 0.156 Angle : 0.527 7.164 23216 Z= 0.272 Chirality : 0.045 0.190 2685 Planarity : 0.005 0.073 2921 Dihedral : 11.904 178.863 2572 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.02 % Favored : 97.84 % Rotamer: Outliers : 1.33 % Allowed : 10.25 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2129 helix: -0.15 (0.18), residues: 720 sheet: -0.82 (0.23), residues: 432 loop : -0.86 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 325 HIS 0.005 0.001 HIS C 441 PHE 0.010 0.001 PHE C 272 TYR 0.017 0.001 TYR C 297 ARG 0.006 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.963 Fit side-chains REVERT: A 126 TYR cc_start: 0.8751 (m-80) cc_final: 0.8302 (m-80) REVERT: B 248 LYS cc_start: 0.8757 (pptt) cc_final: 0.8432 (ptpt) REVERT: C 292 GLN cc_start: 0.8377 (tt0) cc_final: 0.8007 (tt0) REVERT: C 322 ASP cc_start: 0.7845 (m-30) cc_final: 0.7593 (m-30) REVERT: C 342 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8676 (ptm) REVERT: D 84 GLN cc_start: 0.8246 (tp40) cc_final: 0.7980 (mm-40) REVERT: E 108 ARG cc_start: 0.8365 (tpt90) cc_final: 0.7986 (tpp-160) REVERT: E 227 GLN cc_start: 0.8581 (pm20) cc_final: 0.8092 (pm20) REVERT: E 248 LYS cc_start: 0.8756 (pptt) cc_final: 0.8401 (ptpt) REVERT: F 181 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: F 222 MET cc_start: 0.8137 (mmm) cc_final: 0.7337 (mpp) REVERT: F 256 MET cc_start: 0.9030 (ptm) cc_final: 0.8787 (ptp) REVERT: F 369 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8153 (t0) REVERT: F 450 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7789 (tt0) outliers start: 24 outliers final: 11 residues processed: 145 average time/residue: 1.4776 time to fit residues: 236.5125 Evaluate side-chains 142 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 141 HIS D 353 GLN E 16 ASN E 141 HIS F 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17114 Z= 0.256 Angle : 0.560 8.240 23216 Z= 0.288 Chirality : 0.046 0.177 2685 Planarity : 0.005 0.074 2921 Dihedral : 11.496 176.548 2568 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 1.83 % Allowed : 10.53 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2129 helix: 0.56 (0.19), residues: 722 sheet: -0.69 (0.23), residues: 446 loop : -0.71 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 325 HIS 0.006 0.001 HIS C 441 PHE 0.018 0.001 PHE C 272 TYR 0.021 0.001 TYR F 297 ARG 0.007 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 2.048 Fit side-chains REVERT: A 126 TYR cc_start: 0.8746 (m-80) cc_final: 0.8323 (m-80) REVERT: B 227 GLN cc_start: 0.8586 (pm20) cc_final: 0.8116 (pm20) REVERT: B 248 LYS cc_start: 0.8779 (pptt) cc_final: 0.8459 (ptmt) REVERT: C 292 GLN cc_start: 0.8398 (tt0) cc_final: 0.8129 (tt0) REVERT: C 322 ASP cc_start: 0.7950 (m-30) cc_final: 0.7731 (m-30) REVERT: D 84 GLN cc_start: 0.8275 (tp40) cc_final: 0.8051 (mm-40) REVERT: D 126 TYR cc_start: 0.8705 (m-80) cc_final: 0.8321 (m-80) REVERT: E 81 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: E 248 LYS cc_start: 0.8783 (pptt) cc_final: 0.8430 (ptpt) REVERT: F 1 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5607 (ppp) REVERT: F 181 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: F 256 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8815 (ptp) REVERT: F 292 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: F 342 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8253 (ptm) REVERT: F 450 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7852 (tt0) outliers start: 33 outliers final: 15 residues processed: 151 average time/residue: 1.4829 time to fit residues: 246.7653 Evaluate side-chains 146 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 173 optimal weight: 0.4980 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN E 16 ASN E 66 GLN F 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17114 Z= 0.163 Angle : 0.516 8.525 23216 Z= 0.264 Chirality : 0.045 0.174 2685 Planarity : 0.004 0.075 2921 Dihedral : 10.999 175.173 2563 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 1.66 % Allowed : 11.14 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2129 helix: 0.99 (0.20), residues: 720 sheet: -0.57 (0.23), residues: 446 loop : -0.51 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 PHE 0.010 0.001 PHE F 255 TYR 0.015 0.001 TYR C 297 ARG 0.005 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.993 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8695 (m-80) cc_final: 0.8274 (m-80) REVERT: B 81 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: B 162 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.6994 (mpp) REVERT: B 227 GLN cc_start: 0.8534 (pm20) cc_final: 0.8139 (pm20) REVERT: B 248 LYS cc_start: 0.8757 (pptt) cc_final: 0.8457 (ptmt) REVERT: C 292 GLN cc_start: 0.8390 (tt0) cc_final: 0.8159 (tt0) REVERT: C 322 ASP cc_start: 0.7928 (m-30) cc_final: 0.7694 (m-30) REVERT: C 450 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: D 84 GLN cc_start: 0.8255 (tp40) cc_final: 0.8032 (mm-40) REVERT: D 126 TYR cc_start: 0.8671 (m-80) cc_final: 0.8290 (m-80) REVERT: E 209 LYS cc_start: 0.8843 (mmpt) cc_final: 0.8615 (mmmt) REVERT: E 248 LYS cc_start: 0.8782 (pptt) cc_final: 0.8466 (ptpt) REVERT: F 1 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5951 (ppp) REVERT: F 155 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8321 (mtt) REVERT: F 256 MET cc_start: 0.9039 (ptm) cc_final: 0.8788 (ptp) REVERT: F 450 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7844 (tt0) outliers start: 30 outliers final: 10 residues processed: 152 average time/residue: 1.5217 time to fit residues: 255.3201 Evaluate side-chains 144 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN E 66 GLN F 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17114 Z= 0.233 Angle : 0.538 10.095 23216 Z= 0.274 Chirality : 0.046 0.171 2685 Planarity : 0.004 0.075 2921 Dihedral : 10.944 175.208 2562 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.30 % Favored : 97.55 % Rotamer: Outliers : 1.72 % Allowed : 11.25 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2129 helix: 1.13 (0.20), residues: 722 sheet: -0.57 (0.23), residues: 452 loop : -0.46 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 325 HIS 0.005 0.001 HIS C 441 PHE 0.012 0.001 PHE C 272 TYR 0.020 0.001 TYR F 297 ARG 0.004 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.991 Fit side-chains REVERT: A 126 TYR cc_start: 0.8702 (m-80) cc_final: 0.8283 (m-80) REVERT: A 242 PRO cc_start: 0.8934 (Cg_endo) cc_final: 0.8730 (Cg_exo) REVERT: B 81 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: B 248 LYS cc_start: 0.8754 (pptt) cc_final: 0.8473 (ptmt) REVERT: C 292 GLN cc_start: 0.8391 (tt0) cc_final: 0.8165 (tt0) REVERT: C 322 ASP cc_start: 0.7921 (m-30) cc_final: 0.7699 (m-30) REVERT: D 84 GLN cc_start: 0.8255 (tp40) cc_final: 0.8039 (mm-40) REVERT: D 126 TYR cc_start: 0.8693 (m-80) cc_final: 0.8327 (m-80) REVERT: E 248 LYS cc_start: 0.8801 (pptt) cc_final: 0.8422 (ptmt) REVERT: F 1 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6038 (ppp) REVERT: F 94 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: F 155 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: F 342 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8236 (ptm) REVERT: F 450 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7897 (tt0) outliers start: 31 outliers final: 11 residues processed: 151 average time/residue: 1.4855 time to fit residues: 247.8050 Evaluate side-chains 143 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN E 66 GLN F 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17114 Z= 0.229 Angle : 0.543 10.705 23216 Z= 0.277 Chirality : 0.046 0.170 2685 Planarity : 0.004 0.076 2921 Dihedral : 10.829 174.501 2562 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.40 % Favored : 97.46 % Rotamer: Outliers : 1.50 % Allowed : 11.58 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2129 helix: 1.20 (0.20), residues: 724 sheet: -0.48 (0.24), residues: 448 loop : -0.42 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 325 HIS 0.005 0.001 HIS C 441 PHE 0.011 0.001 PHE C 272 TYR 0.019 0.001 TYR F 297 ARG 0.004 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8730 (m-80) cc_final: 0.8298 (m-80) REVERT: B 81 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: B 248 LYS cc_start: 0.8742 (pptt) cc_final: 0.8455 (ptmt) REVERT: C 342 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8276 (ptm) REVERT: C 450 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: D 84 GLN cc_start: 0.8292 (tp40) cc_final: 0.8068 (mm-40) REVERT: D 126 TYR cc_start: 0.8691 (m-80) cc_final: 0.8252 (m-80) REVERT: E 209 LYS cc_start: 0.8889 (mmpt) cc_final: 0.8681 (mmmt) REVERT: E 248 LYS cc_start: 0.8779 (pptt) cc_final: 0.8475 (ptpt) REVERT: F 1 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.6068 (ppp) REVERT: F 181 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: F 342 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8224 (ptm) REVERT: F 450 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7903 (tt0) outliers start: 27 outliers final: 12 residues processed: 155 average time/residue: 1.5309 time to fit residues: 262.2465 Evaluate side-chains 147 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 353 GLN C 292 GLN D 211 ASN D 353 GLN E 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17114 Z= 0.167 Angle : 0.523 7.873 23216 Z= 0.268 Chirality : 0.045 0.168 2685 Planarity : 0.004 0.079 2921 Dihedral : 10.530 173.537 2562 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.27 % Rotamer: Outliers : 1.39 % Allowed : 11.69 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2129 helix: 1.36 (0.20), residues: 724 sheet: -0.47 (0.24), residues: 448 loop : -0.37 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 PHE 0.011 0.001 PHE F 255 TYR 0.016 0.001 TYR F 297 ARG 0.004 0.000 ARG E 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 2.078 Fit side-chains REVERT: A 126 TYR cc_start: 0.8692 (m-80) cc_final: 0.8200 (m-80) REVERT: B 62 MET cc_start: 0.8057 (ttp) cc_final: 0.7802 (ttt) REVERT: B 108 ARG cc_start: 0.8420 (tpt90) cc_final: 0.8015 (tpp-160) REVERT: B 248 LYS cc_start: 0.8736 (pptt) cc_final: 0.8456 (ptmt) REVERT: C 342 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8249 (ptm) REVERT: C 450 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: D 84 GLN cc_start: 0.8250 (tp40) cc_final: 0.8048 (mm-40) REVERT: D 126 TYR cc_start: 0.8678 (m-80) cc_final: 0.8231 (m-80) REVERT: E 26 LEU cc_start: 0.7830 (mm) cc_final: 0.7606 (mm) REVERT: E 62 MET cc_start: 0.8046 (ttp) cc_final: 0.7794 (ttt) REVERT: E 248 LYS cc_start: 0.8789 (pptt) cc_final: 0.8464 (ptmt) REVERT: F 1 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.6059 (ppp) REVERT: F 181 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: F 342 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8219 (ptm) REVERT: F 450 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7861 (tt0) outliers start: 25 outliers final: 9 residues processed: 150 average time/residue: 1.4942 time to fit residues: 247.7830 Evaluate side-chains 142 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN E 66 GLN F 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17114 Z= 0.212 Angle : 0.541 8.425 23216 Z= 0.276 Chirality : 0.046 0.174 2685 Planarity : 0.004 0.074 2921 Dihedral : 10.390 174.122 2562 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.27 % Rotamer: Outliers : 1.22 % Allowed : 12.19 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2129 helix: 1.41 (0.20), residues: 724 sheet: -0.44 (0.24), residues: 448 loop : -0.36 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 325 HIS 0.004 0.001 HIS F 441 PHE 0.010 0.001 PHE C 272 TYR 0.018 0.001 TYR F 297 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.984 Fit side-chains REVERT: B 62 MET cc_start: 0.8149 (ttp) cc_final: 0.7913 (ttt) REVERT: B 108 ARG cc_start: 0.8447 (tpt90) cc_final: 0.8036 (tpp80) REVERT: B 162 MET cc_start: 0.8012 (mpp) cc_final: 0.7754 (mmm) REVERT: B 248 LYS cc_start: 0.8739 (pptt) cc_final: 0.8480 (ptmt) REVERT: C 342 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8792 (ppp) REVERT: C 450 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: D 126 TYR cc_start: 0.8690 (m-80) cc_final: 0.8247 (m-80) REVERT: E 108 ARG cc_start: 0.8355 (tpt90) cc_final: 0.8013 (tpp80) REVERT: E 248 LYS cc_start: 0.8814 (pptt) cc_final: 0.8470 (ptmt) REVERT: F 1 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.6101 (ppp) REVERT: F 181 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: F 342 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8243 (ptm) REVERT: F 450 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7881 (tt0) outliers start: 22 outliers final: 10 residues processed: 145 average time/residue: 1.5377 time to fit residues: 246.4513 Evaluate side-chains 143 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 0.0030 chunk 17 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN F 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17114 Z= 0.195 Angle : 0.544 12.838 23216 Z= 0.277 Chirality : 0.045 0.165 2685 Planarity : 0.004 0.074 2921 Dihedral : 10.336 174.233 2562 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Rotamer: Outliers : 1.11 % Allowed : 12.52 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 2129 helix: 1.45 (0.20), residues: 724 sheet: -0.42 (0.24), residues: 448 loop : -0.35 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 325 HIS 0.004 0.001 HIS C 441 PHE 0.010 0.001 PHE F 255 TYR 0.016 0.001 TYR C 297 ARG 0.003 0.000 ARG B 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.998 Fit side-chains REVERT: A 126 TYR cc_start: 0.8746 (m-80) cc_final: 0.8384 (m-80) REVERT: B 62 MET cc_start: 0.8109 (ttp) cc_final: 0.7881 (ttt) REVERT: B 108 ARG cc_start: 0.8449 (tpt90) cc_final: 0.8058 (tpp80) REVERT: B 162 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7713 (mmm) REVERT: B 248 LYS cc_start: 0.8748 (pptt) cc_final: 0.8519 (ptmt) REVERT: C 342 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8787 (ppp) REVERT: C 450 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: D 126 TYR cc_start: 0.8690 (m-80) cc_final: 0.8245 (m-80) REVERT: E 108 ARG cc_start: 0.8383 (tpt90) cc_final: 0.8028 (tpp80) REVERT: E 162 MET cc_start: 0.7981 (mpp) cc_final: 0.7751 (mmm) REVERT: E 248 LYS cc_start: 0.8791 (pptt) cc_final: 0.8469 (ptmt) REVERT: F 1 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.6075 (ppp) REVERT: F 181 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: F 342 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8242 (ptm) REVERT: F 450 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7855 (tt0) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 1.5802 time to fit residues: 251.2040 Evaluate side-chains 144 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 0.0070 chunk 69 optimal weight: 0.4980 chunk 171 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.064672 restraints weight = 33584.245| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.64 r_work: 0.2721 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17114 Z= 0.155 Angle : 0.524 8.761 23216 Z= 0.267 Chirality : 0.044 0.167 2685 Planarity : 0.004 0.073 2921 Dihedral : 10.189 172.748 2562 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.27 % Rotamer: Outliers : 1.05 % Allowed : 12.69 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 2129 helix: 1.53 (0.20), residues: 724 sheet: -0.43 (0.24), residues: 448 loop : -0.32 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 325 HIS 0.003 0.001 HIS C 441 PHE 0.012 0.001 PHE F 255 TYR 0.014 0.001 TYR C 297 ARG 0.003 0.000 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5815.47 seconds wall clock time: 102 minutes 47.40 seconds (6167.40 seconds total)