Starting phenix.real_space_refine on Sun Feb 18 15:43:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/02_2024/6lar_0862.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/02_2024/6lar_0862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/02_2024/6lar_0862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/02_2024/6lar_0862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/02_2024/6lar_0862.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/02_2024/6lar_0862.pdb" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 14396 2.51 5 N 4020 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F GLU 25": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F ARG 366": "NH1" <-> "NH2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "G ARG 4": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G ARG 264": "NH1" <-> "NH2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "J ARG 10": "NH1" <-> "NH2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J ARG 214": "NH1" <-> "NH2" Residue "J GLU 223": "OE1" <-> "OE2" Residue "J GLU 288": "OE1" <-> "OE2" Residue "J GLU 345": "OE1" <-> "OE2" Residue "J ARG 369": "NH1" <-> "NH2" Residue "J GLU 389": "OE1" <-> "OE2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22448 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "B" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3055 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 2 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2667 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 29, 'TRANS': 306} Chain breaks: 4 Chain: "G" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Chain: "E" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3055 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 2 Chain: "H" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "I" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 461 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "J" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2574 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 26, 'TRANS': 297} Chain breaks: 4 Chain: "D" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Time building chain proxies: 11.35, per 1000 atoms: 0.51 Number of scatterers: 22448 At special positions: 0 Unit cell: (183.68, 153.34, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3976 8.00 N 4020 7.00 C 14396 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 - 3.50 Amino acid : False - 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: 8.43 Conformation dependent library (CDL) restraints added in 4.0 seconds 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 17 sheets defined 56.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.868A pdb=" N THR A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 removed outlier: 4.238A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 130 through 158 removed outlier: 4.043A pdb=" N ARG B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 4.081A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.807A pdb=" N SER B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.611A pdb=" N VAL B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 235 removed outlier: 3.777A pdb=" N GLY B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 263 removed outlier: 3.515A pdb=" N PHE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 285 removed outlier: 3.930A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.696A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 319 through 350 removed outlier: 3.924A pdb=" N ARG B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.657A pdb=" N TRP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL B 364 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 removed outlier: 4.559A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 removed outlier: 4.173A pdb=" N ASN B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 455 removed outlier: 4.025A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 4.333A pdb=" N VAL B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 114 through 124 removed outlier: 4.218A pdb=" N ILE C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 158 removed outlier: 4.436A pdb=" N ARG C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 181 removed outlier: 3.852A pdb=" N VAL C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 196 through 207 removed outlier: 3.751A pdb=" N VAL C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 3.633A pdb=" N ALA C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 264 removed outlier: 4.098A pdb=" N THR C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.709A pdb=" N ARG C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 319 removed outlier: 3.603A pdb=" N LEU C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.834A pdb=" N ARG C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.961A pdb=" N VAL C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 374 removed outlier: 3.718A pdb=" N TRP C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.770A pdb=" N HIS C 389 " --> pdb=" O TRP C 385 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 435 through 439 removed outlier: 3.544A pdb=" N TYR C 439 " --> pdb=" O PRO C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 467 removed outlier: 3.796A pdb=" N ASP C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix Processing helix chain 'C' and resid 467 through 472 removed outlier: 4.029A pdb=" N VAL C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 93 through 130 removed outlier: 3.946A pdb=" N VAL F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 Processing helix chain 'F' and resid 183 through 194 removed outlier: 4.007A pdb=" N ALA F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 239 removed outlier: 3.553A pdb=" N ALA F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 386 through 398 Processing helix chain 'G' and resid 2 through 17 removed outlier: 3.840A pdb=" N LEU G 17 " --> pdb=" O VAL G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 41 removed outlier: 3.747A pdb=" N ILE G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 62 Processing helix chain 'G' and resid 86 through 89 Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.624A pdb=" N ARG G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 163 Processing helix chain 'G' and resid 206 through 212 Processing helix chain 'G' and resid 265 through 269 removed outlier: 3.726A pdb=" N ALA G 269 " --> pdb=" O PRO G 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 265 through 269' Processing helix chain 'E' and resid 34 through 46 removed outlier: 4.165A pdb=" N ILE E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Proline residue: E 40 - end of helix removed outlier: 3.683A pdb=" N ARG E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.972A pdb=" N VAL E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.638A pdb=" N THR E 130 " --> pdb=" O TRP E 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS E 131 " --> pdb=" O GLY E 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 131' Processing helix chain 'E' and resid 132 through 157 removed outlier: 3.690A pdb=" N GLY E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 181 removed outlier: 3.704A pdb=" N LEU E 179 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 205 removed outlier: 3.531A pdb=" N VAL E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 195 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Proline residue: E 199 - end of helix removed outlier: 3.683A pdb=" N ALA E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 233 removed outlier: 3.554A pdb=" N ALA E 221 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 231 " --> pdb=" O TRP E 227 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 263 removed outlier: 4.001A pdb=" N PHE E 244 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA E 261 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 removed outlier: 4.391A pdb=" N CYS E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 277 " --> pdb=" O CYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 293 removed outlier: 3.581A pdb=" N TRP E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 294 No H-bonds generated for 'chain 'E' and resid 294 through 294' Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 319 through 350 removed outlier: 3.612A pdb=" N ARG E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 325 " --> pdb=" O PRO E 321 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 346 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.677A pdb=" N TYR E 361 " --> pdb=" O PRO E 357 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 366 " --> pdb=" O ILE E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 377 removed outlier: 3.778A pdb=" N VAL E 376 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 388 removed outlier: 3.684A pdb=" N LYS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU E 386 " --> pdb=" O CYS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 404 Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.933A pdb=" N TRP E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN E 430 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 453 removed outlier: 3.855A pdb=" N GLY E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 466 removed outlier: 3.555A pdb=" N LEU E 464 " --> pdb=" O PRO E 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 466 " --> pdb=" O MET E 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 37 removed outlier: 3.591A pdb=" N GLU H 37 " --> pdb=" O PRO H 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 34 through 37' Processing helix chain 'H' and resid 38 through 47 removed outlier: 3.817A pdb=" N VAL H 42 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 removed outlier: 3.663A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 124 removed outlier: 4.005A pdb=" N PHE H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 156 removed outlier: 3.920A pdb=" N ALA H 133 " --> pdb=" O PRO H 129 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 181 removed outlier: 3.684A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 196 removed outlier: 4.490A pdb=" N THR H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 208 removed outlier: 3.880A pdb=" N ALA H 202 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA H 205 " --> pdb=" O ALA H 201 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU H 206 " --> pdb=" O ALA H 202 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL H 208 " --> pdb=" O PHE H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.926A pdb=" N LEU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 264 removed outlier: 3.748A pdb=" N THR H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 249 " --> pdb=" O THR H 245 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU H 263 " --> pdb=" O GLY H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 285 removed outlier: 3.584A pdb=" N LEU H 277 " --> pdb=" O CYS H 273 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 278 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL H 282 " --> pdb=" O LEU H 278 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 294 removed outlier: 3.671A pdb=" N TRP H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA H 294 " --> pdb=" O SER H 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 289 through 294' Processing helix chain 'H' and resid 316 through 318 No H-bonds generated for 'chain 'H' and resid 316 through 318' Processing helix chain 'H' and resid 319 through 351 removed outlier: 3.994A pdb=" N ARG H 325 " --> pdb=" O PRO H 321 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA H 329 " --> pdb=" O ARG H 325 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 332 " --> pdb=" O GLN H 328 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER H 346 " --> pdb=" O GLY H 342 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU H 349 " --> pdb=" O GLY H 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 370 removed outlier: 4.028A pdb=" N VAL H 364 " --> pdb=" O TRP H 360 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 367 " --> pdb=" O VAL H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 403 removed outlier: 3.707A pdb=" N TRP H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU H 386 " --> pdb=" O CYS H 382 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS H 389 " --> pdb=" O TRP H 385 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA H 400 " --> pdb=" O ALA H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 429 removed outlier: 4.128A pdb=" N TRP H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 457 removed outlier: 3.783A pdb=" N GLY H 448 " --> pdb=" O ARG H 444 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP H 455 " --> pdb=" O ALA H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 467 Processing helix chain 'H' and resid 468 through 471 Processing helix chain 'I' and resid 34 through 55 removed outlier: 3.885A pdb=" N PHE I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA I 49 " --> pdb=" O MET I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 87 removed outlier: 3.783A pdb=" N THR I 66 " --> pdb=" O ASP I 62 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL I 71 " --> pdb=" O GLN I 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA I 75 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU I 76 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU I 78 " --> pdb=" O GLY I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 113 removed outlier: 3.790A pdb=" N VAL J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 99 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA J 102 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP J 103 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR J 107 " --> pdb=" O ASP J 103 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL J 110 " --> pdb=" O ARG J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 129 removed outlier: 3.769A pdb=" N HIS J 118 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA J 119 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 138 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.623A pdb=" N ALA J 189 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 212 removed outlier: 3.846A pdb=" N LYS J 211 " --> pdb=" O ASP J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 238 removed outlier: 3.843A pdb=" N ARG J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN J 234 " --> pdb=" O ALA J 230 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP J 238 " --> pdb=" O GLN J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 263 removed outlier: 3.582A pdb=" N TRP J 260 " --> pdb=" O ASP J 257 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP J 263 " --> pdb=" O TRP J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 292 removed outlier: 3.517A pdb=" N GLU J 291 " --> pdb=" O ALA J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 398 removed outlier: 3.705A pdb=" N HIS J 392 " --> pdb=" O ALA J 388 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE J 393 " --> pdb=" O GLU J 389 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 394 " --> pdb=" O ALA J 390 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG J 396 " --> pdb=" O HIS J 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.839A pdb=" N LEU D 17 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 41 removed outlier: 3.746A pdb=" N ILE D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 89 Processing helix chain 'D' and resid 90 through 95 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.625A pdb=" N ARG D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'D' and resid 265 through 269 removed outlier: 3.725A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 269' Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.664A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 14 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 25 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 16 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.592A pdb=" N LEU C 94 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA C 13 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.550A pdb=" N GLN C 97 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 23 through 24 removed outlier: 3.616A pdb=" N ILE F 24 " --> pdb=" O LYS F 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'F' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'F' and resid 244 through 247 removed outlier: 6.035A pdb=" N LEU F 314 " --> pdb=" O THR F 338 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE F 340 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL F 316 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU F 360 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR F 216 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL F 362 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE F 218 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 166 through 169 removed outlier: 4.444A pdb=" N VAL G 79 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA G 76 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL G 82 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER G 120 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR G 125 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS G 106 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU G 225 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL G 241 " --> pdb=" O ALA G 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 9 through 16 removed outlier: 3.835A pdb=" N THR E 25 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 Processing sheet with id=AB2, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.078A pdb=" N ALA H 13 " --> pdb=" O LEU H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'J' and resid 4 through 5 removed outlier: 5.957A pdb=" N LEU J 4 " --> pdb=" O ASP J 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 158 through 165 removed outlier: 7.249A pdb=" N THR J 205 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG J 162 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA J 203 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP J 164 " --> pdb=" O ARG J 201 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG J 201 " --> pdb=" O ASP J 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 342 through 343 removed outlier: 6.516A pdb=" N VAL J 217 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 244 through 249 Processing sheet with id=AB8, first strand: chain 'D' and resid 166 through 169 removed outlier: 4.444A pdb=" N VAL D 79 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 76 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL D 82 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER D 120 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 125 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 106 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 225 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 241 " --> pdb=" O ALA D 195 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3378 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: 7.06 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7128 1.33 - 1.45: 3399 1.45 - 1.57: 12246 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 22871 Sorted by residual: bond pdb=" N ILE J 22 " pdb=" CA ILE J 22 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.22e+00 bond pdb=" N ILE J 180 " pdb=" CA ILE J 180 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.25e-02 6.40e+03 8.68e+00 bond pdb=" N VAL J 111 " pdb=" CA VAL J 111 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.54e+00 bond pdb=" N VAL E 395 " pdb=" CA VAL E 395 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N VAL A 19 " pdb=" CA VAL A 19 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.36e+00 ... (remaining 22866 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.57: 653 105.57 - 112.75: 13183 112.75 - 119.92: 7673 119.92 - 127.10: 9465 127.10 - 134.28: 343 Bond angle restraints: 31317 Sorted by residual: angle pdb=" CA GLU G 232 " pdb=" CB GLU G 232 " pdb=" CG GLU G 232 " ideal model delta sigma weight residual 114.10 129.01 -14.91 2.00e+00 2.50e-01 5.56e+01 angle pdb=" CA GLU D 232 " pdb=" CB GLU D 232 " pdb=" CG GLU D 232 " ideal model delta sigma weight residual 114.10 128.94 -14.84 2.00e+00 2.50e-01 5.51e+01 angle pdb=" N VAL E 86 " pdb=" CA VAL E 86 " pdb=" C VAL E 86 " ideal model delta sigma weight residual 112.83 105.95 6.88 9.90e-01 1.02e+00 4.84e+01 angle pdb=" CB GLU D 232 " pdb=" CG GLU D 232 " pdb=" CD GLU D 232 " ideal model delta sigma weight residual 112.60 122.05 -9.45 1.70e+00 3.46e-01 3.09e+01 angle pdb=" CB GLU G 232 " pdb=" CG GLU G 232 " pdb=" CD GLU G 232 " ideal model delta sigma weight residual 112.60 122.02 -9.42 1.70e+00 3.46e-01 3.07e+01 ... (remaining 31312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12176 17.94 - 35.89: 1156 35.89 - 53.83: 272 53.83 - 71.77: 70 71.77 - 89.71: 12 Dihedral angle restraints: 13686 sinusoidal: 5053 harmonic: 8633 Sorted by residual: dihedral pdb=" CA ALA J 323 " pdb=" C ALA J 323 " pdb=" N ASP J 324 " pdb=" CA ASP J 324 " ideal model delta harmonic sigma weight residual 180.00 149.27 30.73 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA VAL B 208 " pdb=" C VAL B 208 " pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta harmonic sigma weight residual 180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA PRO B 100 " pdb=" C PRO B 100 " pdb=" N SER B 101 " pdb=" CA SER B 101 " ideal model delta harmonic sigma weight residual 180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 13683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2717 0.048 - 0.096: 921 0.096 - 0.144: 219 0.144 - 0.193: 36 0.193 - 0.241: 3 Chirality restraints: 3896 Sorted by residual: chirality pdb=" CA GLN E 408 " pdb=" N GLN E 408 " pdb=" C GLN E 408 " pdb=" CB GLN E 408 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE J 24 " pdb=" N ILE J 24 " pdb=" C ILE J 24 " pdb=" CB ILE J 24 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL J 173 " pdb=" N VAL J 173 " pdb=" C VAL J 173 " pdb=" CB VAL J 173 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3893 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU G 232 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" CD GLU G 232 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU G 232 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU G 232 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 232 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.15e+00 pdb=" CD GLU D 232 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU D 232 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU D 232 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL J 165 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO J 166 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO J 166 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 166 " -0.036 5.00e-02 4.00e+02 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 138 2.47 - 3.08: 17190 3.08 - 3.68: 33559 3.68 - 4.29: 45813 4.29 - 4.90: 72711 Nonbonded interactions: 169411 Sorted by model distance: nonbonded pdb=" OG SER E 346 " pdb=" CG1 VAL E 363 " model vdw 1.858 3.460 nonbonded pdb=" NE ARG E 107 " pdb=" NH2 ARG J 116 " model vdw 2.015 3.200 nonbonded pdb=" OG1 THR J 94 " pdb=" OE2 GLU J 95 " model vdw 2.037 2.440 nonbonded pdb=" NE2 HIS J 341 " pdb=" OG1 THR J 343 " model vdw 2.080 2.520 nonbonded pdb=" OE2 GLU F 127 " pdb=" NH2 ARG F 162 " model vdw 2.101 2.520 ... (remaining 169406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'C' and (resid 8 through 294 or resid 316 through 471)) selection = (chain 'E' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'H' and (resid 8 through 294 or resid 316 through 471)) } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'F' and (resid 2 through 32 or resid 92 through 297 or resid 311 through \ 401)) selection = (chain 'J' and resid 2 through 401) } 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=0.91 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 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: 0.020 Extract box with map and model: 18.250 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 56.650 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.120 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.007 0.071 22871 Z= 0.486 Angle : 0.988 14.907 31317 Z= 0.579 Chirality : 0.051 0.241 3896 Planarity : 0.006 0.065 3952 Dihedral : 15.429 89.714 8062 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.22 % Favored : 86.41 % Rotamer: Outliers : 5.47 % Allowed : 12.98 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.82 (0.13), residues: 2936 helix: -2.70 (0.10), residues: 1497 sheet: -2.16 (0.31), residues: 258 loop : -4.04 (0.15), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 231 HIS 0.010 0.002 HIS E 330 PHE 0.021 0.002 PHE A 88 TYR 0.020 0.002 TYR J 352 ARG 0.008 0.001 ARG J 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 467 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.8258 (ptp) cc_final: 0.8037 (ptp) REVERT: B 277 LEU cc_start: 0.8975 (tt) cc_final: 0.8603 (mm) REVERT: B 372 LEU cc_start: 0.8458 (tp) cc_final: 0.8237 (tp) REVERT: B 433 ILE cc_start: 0.8046 (mp) cc_final: 0.7792 (mm) REVERT: C 44 ARG cc_start: 0.6773 (ptp90) cc_final: 0.5966 (mmp-170) REVERT: C 411 LEU cc_start: 0.8090 (pp) cc_final: 0.7188 (tp) REVERT: F 352 TYR cc_start: 0.7666 (m-80) cc_final: 0.7400 (t80) REVERT: F 397 LEU cc_start: 0.8751 (pp) cc_final: 0.8210 (tp) REVERT: G 29 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6237 (m) REVERT: G 165 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8282 (p) REVERT: E 38 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8687 (pt) REVERT: E 277 LEU cc_start: 0.8800 (mt) cc_final: 0.8586 (mt) REVERT: E 407 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: E 432 LYS cc_start: 0.8005 (tttt) cc_final: 0.7671 (mmtm) REVERT: E 462 MET cc_start: 0.7897 (tpp) cc_final: 0.7673 (tpt) REVERT: E 469 PHE cc_start: 0.6926 (p90) cc_final: 0.6595 (p90) REVERT: H 120 SER cc_start: 0.8729 (p) cc_final: 0.7267 (t) REVERT: I 45 MET cc_start: 0.7674 (mmm) cc_final: 0.7244 (tmm) REVERT: J 96 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7952 (tp30) REVERT: J 111 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8955 (p) REVERT: D 267 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7693 (mp) REVERT: D 276 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7567 (tm-30) outliers start: 126 outliers final: 51 residues processed: 557 average time/residue: 0.3724 time to fit residues: 309.5393 Evaluate side-chains 373 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 315 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 238 CYS Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 389 HIS Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 112 ARG Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 276 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 0.1980 chunk 225 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 131 HIS C 154 HIS ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN F 8 HIS F 122 GLN F 371 GLN E 164 GLN H 131 HIS ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 HIS J 122 GLN J 187 HIS J 271 ASN J 371 GLN J 376 GLN D 162 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 22871 Z= 0.235 Angle : 0.764 8.587 31317 Z= 0.377 Chirality : 0.044 0.285 3896 Planarity : 0.006 0.061 3952 Dihedral : 7.843 58.549 3342 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.78 % Favored : 90.16 % Rotamer: Outliers : 5.04 % Allowed : 18.71 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.90 (0.15), residues: 2936 helix: -0.85 (0.12), residues: 1600 sheet: -1.94 (0.29), residues: 273 loop : -3.59 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 21 HIS 0.006 0.001 HIS C 154 PHE 0.015 0.002 PHE C 77 TYR 0.022 0.002 TYR G 100 ARG 0.009 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 395 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ILE cc_start: 0.8073 (mp) cc_final: 0.7833 (mm) REVERT: B 449 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7230 (t80) REVERT: C 44 ARG cc_start: 0.6701 (ptp90) cc_final: 0.5990 (mmp-170) REVERT: C 277 LEU cc_start: 0.7922 (mm) cc_final: 0.7675 (mm) REVERT: C 411 LEU cc_start: 0.7896 (pp) cc_final: 0.6970 (tp) REVERT: F 228 ILE cc_start: 0.9022 (mt) cc_final: 0.8499 (tp) REVERT: F 231 TRP cc_start: 0.8232 (p90) cc_final: 0.7327 (p90) REVERT: F 318 LEU cc_start: 0.8025 (mp) cc_final: 0.7661 (tp) REVERT: F 397 LEU cc_start: 0.8530 (pp) cc_final: 0.8172 (tp) REVERT: G 200 LYS cc_start: 0.8286 (tppt) cc_final: 0.7926 (tptp) REVERT: E 212 PHE cc_start: 0.3080 (OUTLIER) cc_final: 0.2670 (m-80) REVERT: E 407 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: E 432 LYS cc_start: 0.7952 (tttt) cc_final: 0.7573 (mmtm) REVERT: H 441 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8106 (tt) REVERT: I 45 MET cc_start: 0.7729 (mmm) cc_final: 0.7502 (tmm) REVERT: J 96 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7311 (tm-30) REVERT: J 111 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8945 (p) REVERT: J 364 ASP cc_start: 0.7436 (p0) cc_final: 0.7194 (p0) REVERT: D 267 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7324 (mp) outliers start: 116 outliers final: 75 residues processed: 470 average time/residue: 0.3057 time to fit residues: 226.8728 Evaluate side-chains 403 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 322 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 162 GLN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.0170 chunk 83 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 292 optimal weight: 0.0270 chunk 241 optimal weight: 5.9990 chunk 268 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN G 22 GLN ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22871 Z= 0.333 Angle : 0.782 11.173 31317 Z= 0.386 Chirality : 0.044 0.294 3896 Planarity : 0.006 0.062 3952 Dihedral : 6.931 58.924 3292 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.00 % Favored : 88.93 % Rotamer: Outliers : 6.17 % Allowed : 23.88 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.37 (0.15), residues: 2936 helix: -0.34 (0.13), residues: 1603 sheet: -1.94 (0.29), residues: 273 loop : -3.42 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 121 HIS 0.011 0.001 HIS C 154 PHE 0.014 0.002 PHE C 204 TYR 0.013 0.002 TYR J 281 ARG 0.020 0.001 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 332 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.4670 (t80) REVERT: B 264 TRP cc_start: 0.7119 (m-90) cc_final: 0.6669 (m-10) REVERT: B 433 ILE cc_start: 0.8095 (mp) cc_final: 0.7832 (mm) REVERT: B 449 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7196 (t80) REVERT: C 27 MET cc_start: 0.3425 (tpt) cc_final: 0.2994 (ttm) REVERT: C 277 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7666 (mm) REVERT: C 285 GLN cc_start: 0.6997 (tm-30) cc_final: 0.6750 (tm-30) REVERT: C 392 LEU cc_start: 0.7788 (tt) cc_final: 0.7575 (tt) REVERT: C 411 LEU cc_start: 0.7963 (pp) cc_final: 0.7102 (tp) REVERT: F 318 LEU cc_start: 0.8001 (mp) cc_final: 0.7713 (tp) REVERT: F 397 LEU cc_start: 0.8679 (pp) cc_final: 0.8272 (tp) REVERT: G 200 LYS cc_start: 0.8557 (tppt) cc_final: 0.7949 (tptp) REVERT: E 212 PHE cc_start: 0.2893 (OUTLIER) cc_final: 0.2435 (m-80) REVERT: E 407 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: E 432 LYS cc_start: 0.8049 (tttt) cc_final: 0.7693 (mmtm) REVERT: E 469 PHE cc_start: 0.7360 (p90) cc_final: 0.6836 (p90) REVERT: I 45 MET cc_start: 0.7680 (mmm) cc_final: 0.7349 (tmm) REVERT: J 96 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7190 (tm-30) REVERT: J 364 ASP cc_start: 0.7479 (p0) cc_final: 0.7108 (p0) REVERT: D 121 TRP cc_start: 0.7372 (m100) cc_final: 0.6991 (m100) REVERT: D 267 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7300 (mp) outliers start: 142 outliers final: 99 residues processed: 429 average time/residue: 0.2928 time to fit residues: 203.3961 Evaluate side-chains 413 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 308 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 0.8980 chunk 203 optimal weight: 0.0270 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN G 22 GLN E 330 HIS ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22871 Z= 0.183 Angle : 0.692 12.820 31317 Z= 0.335 Chirality : 0.042 0.288 3896 Planarity : 0.005 0.054 3952 Dihedral : 6.219 59.329 3283 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.13 % Favored : 90.80 % Rotamer: Outliers : 3.56 % Allowed : 26.92 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.61 (0.16), residues: 2936 helix: 0.38 (0.13), residues: 1591 sheet: -1.73 (0.29), residues: 279 loop : -3.19 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 231 HIS 0.009 0.001 HIS C 154 PHE 0.017 0.001 PHE H 165 TYR 0.018 0.001 TYR G 96 ARG 0.011 0.000 ARG H 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 368 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8556 (mmt) cc_final: 0.8333 (mmt) REVERT: A 88 PHE cc_start: 0.4864 (OUTLIER) cc_final: 0.4598 (t80) REVERT: B 138 LEU cc_start: 0.8616 (tt) cc_final: 0.8051 (mt) REVERT: B 264 TRP cc_start: 0.7039 (m-90) cc_final: 0.6345 (m-10) REVERT: B 433 ILE cc_start: 0.7981 (mp) cc_final: 0.7742 (mm) REVERT: B 449 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7079 (t80) REVERT: C 27 MET cc_start: 0.3417 (tpt) cc_final: 0.2815 (ttt) REVERT: C 277 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7698 (mm) REVERT: C 285 GLN cc_start: 0.6984 (tm-30) cc_final: 0.6413 (tm-30) REVERT: C 411 LEU cc_start: 0.7864 (pp) cc_final: 0.6967 (tp) REVERT: F 318 LEU cc_start: 0.8013 (mp) cc_final: 0.7804 (tp) REVERT: F 370 TRP cc_start: 0.5639 (t-100) cc_final: 0.5434 (t-100) REVERT: F 397 LEU cc_start: 0.8502 (pp) cc_final: 0.8196 (tp) REVERT: G 22 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6326 (pm20) REVERT: G 200 LYS cc_start: 0.8561 (tppt) cc_final: 0.8172 (mmmt) REVERT: G 226 PHE cc_start: 0.8055 (m-80) cc_final: 0.7748 (m-80) REVERT: E 407 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: E 432 LYS cc_start: 0.8009 (tttt) cc_final: 0.7633 (mmtm) REVERT: E 445 ARG cc_start: 0.8226 (mmp80) cc_final: 0.7963 (mmp80) REVERT: H 420 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8046 (mm) REVERT: J 111 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8895 (p) REVERT: J 364 ASP cc_start: 0.7446 (p0) cc_final: 0.7099 (p0) REVERT: J 396 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7542 (mtp85) REVERT: D 267 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7218 (mp) outliers start: 82 outliers final: 48 residues processed: 427 average time/residue: 0.3032 time to fit residues: 207.5639 Evaluate side-chains 380 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 324 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 389 HIS H 126 GLN ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 HIS D 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22871 Z= 0.341 Angle : 0.783 13.498 31317 Z= 0.385 Chirality : 0.045 0.284 3896 Planarity : 0.006 0.080 3952 Dihedral : 6.215 56.599 3273 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.59 % Favored : 89.34 % Rotamer: Outliers : 7.03 % Allowed : 26.18 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.70 (0.16), residues: 2936 helix: 0.20 (0.13), residues: 1605 sheet: -1.58 (0.30), residues: 271 loop : -3.13 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 293 HIS 0.010 0.001 HIS C 154 PHE 0.015 0.002 PHE C 204 TYR 0.020 0.002 TYR G 96 ARG 0.040 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 323 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8185 (tt) REVERT: B 264 TRP cc_start: 0.7006 (m-90) cc_final: 0.6156 (m-10) REVERT: B 449 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7161 (t80) REVERT: C 27 MET cc_start: 0.3503 (tpt) cc_final: 0.3232 (ttm) REVERT: C 44 ARG cc_start: 0.6427 (mtm180) cc_final: 0.5282 (mmp-170) REVERT: C 277 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7678 (mm) REVERT: C 285 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6510 (tm-30) REVERT: C 411 LEU cc_start: 0.8005 (pp) cc_final: 0.7114 (tp) REVERT: F 318 LEU cc_start: 0.8051 (mp) cc_final: 0.7811 (tp) REVERT: F 397 LEU cc_start: 0.8651 (pp) cc_final: 0.8321 (tp) REVERT: G 200 LYS cc_start: 0.8595 (tppt) cc_final: 0.8234 (mmmt) REVERT: E 132 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7436 (mt) REVERT: E 212 PHE cc_start: 0.2676 (OUTLIER) cc_final: 0.2266 (m-80) REVERT: E 407 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: E 432 LYS cc_start: 0.8001 (tttt) cc_final: 0.7677 (mmtm) REVERT: I 45 MET cc_start: 0.7709 (tpt) cc_final: 0.7435 (tmm) REVERT: J 364 ASP cc_start: 0.7522 (p0) cc_final: 0.7155 (p0) REVERT: D 96 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7982 (t80) outliers start: 162 outliers final: 117 residues processed: 438 average time/residue: 0.2956 time to fit residues: 210.8191 Evaluate side-chains 429 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 305 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 346 SER Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 239 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22871 Z= 0.229 Angle : 0.719 15.202 31317 Z= 0.346 Chirality : 0.042 0.276 3896 Planarity : 0.005 0.061 3952 Dihedral : 5.847 55.550 3271 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.57 % Favored : 90.36 % Rotamer: Outliers : 5.17 % Allowed : 27.92 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.36 (0.16), residues: 2936 helix: 0.53 (0.13), residues: 1592 sheet: -1.50 (0.30), residues: 279 loop : -3.01 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 231 HIS 0.008 0.001 HIS C 154 PHE 0.012 0.001 PHE H 165 TYR 0.020 0.002 TYR G 96 ARG 0.009 0.000 ARG F 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 338 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8425 (tt) REVERT: B 264 TRP cc_start: 0.6991 (m-90) cc_final: 0.6256 (m-10) REVERT: B 449 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7100 (t80) REVERT: C 44 ARG cc_start: 0.6545 (mtm180) cc_final: 0.5346 (mmp-170) REVERT: C 204 PHE cc_start: 0.8021 (t80) cc_final: 0.7685 (t80) REVERT: C 277 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7677 (mm) REVERT: C 285 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6438 (tm-30) REVERT: C 411 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7003 (tp) REVERT: F 318 LEU cc_start: 0.8037 (mp) cc_final: 0.7831 (tp) REVERT: F 397 LEU cc_start: 0.8680 (pp) cc_final: 0.8367 (tp) REVERT: G 200 LYS cc_start: 0.8595 (tppt) cc_final: 0.8270 (mmmt) REVERT: E 267 SER cc_start: 0.6845 (t) cc_final: 0.6557 (p) REVERT: E 271 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8165 (mp) REVERT: E 432 LYS cc_start: 0.7959 (tttt) cc_final: 0.7648 (mmtm) REVERT: H 420 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8109 (mm) REVERT: J 223 GLU cc_start: 0.7251 (pt0) cc_final: 0.6496 (pt0) REVERT: J 364 ASP cc_start: 0.7589 (p0) cc_final: 0.7195 (p0) outliers start: 119 outliers final: 83 residues processed: 413 average time/residue: 0.2892 time to fit residues: 197.8232 Evaluate side-chains 399 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 310 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 287 optimal weight: 0.3980 chunk 179 optimal weight: 2.9990 chunk 175 optimal weight: 0.0770 chunk 132 optimal weight: 9.9990 overall best weight: 1.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN E 331 GLN ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22871 Z= 0.231 Angle : 0.726 15.006 31317 Z= 0.350 Chirality : 0.042 0.266 3896 Planarity : 0.005 0.064 3952 Dihedral : 5.493 54.882 3263 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.29 % Favored : 89.65 % Rotamer: Outliers : 5.78 % Allowed : 28.14 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.21 (0.16), residues: 2936 helix: 0.63 (0.13), residues: 1592 sheet: -1.30 (0.31), residues: 269 loop : -2.95 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 21 HIS 0.005 0.001 HIS J 266 PHE 0.016 0.001 PHE E 469 TYR 0.027 0.002 TYR B 407 ARG 0.008 0.000 ARG H 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 333 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8454 (tt) REVERT: B 264 TRP cc_start: 0.6977 (m-90) cc_final: 0.6238 (m-10) REVERT: B 449 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7082 (t80) REVERT: C 44 ARG cc_start: 0.6539 (mtm180) cc_final: 0.5358 (mmp-170) REVERT: C 204 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7674 (t80) REVERT: C 277 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7682 (mm) REVERT: C 285 GLN cc_start: 0.7155 (tm-30) cc_final: 0.6439 (tm-30) REVERT: C 411 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.6976 (tp) REVERT: F 231 TRP cc_start: 0.8102 (p90) cc_final: 0.7461 (p90) REVERT: F 397 LEU cc_start: 0.8705 (pp) cc_final: 0.8380 (tp) REVERT: G 200 LYS cc_start: 0.8563 (tppt) cc_final: 0.8270 (mmmt) REVERT: E 271 ILE cc_start: 0.8415 (mp) cc_final: 0.8143 (mp) REVERT: E 407 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: E 432 LYS cc_start: 0.7952 (tttt) cc_final: 0.7642 (mmtm) REVERT: H 441 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8303 (tt) REVERT: J 364 ASP cc_start: 0.7577 (p0) cc_final: 0.7237 (p0) REVERT: D 96 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7909 (t80) outliers start: 133 outliers final: 94 residues processed: 424 average time/residue: 0.2810 time to fit residues: 196.1410 Evaluate side-chains 409 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 307 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain D residue 21 TRP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 chunk 182 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN E 331 GLN J 122 GLN D 158 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22871 Z= 0.272 Angle : 0.759 15.165 31317 Z= 0.367 Chirality : 0.043 0.244 3896 Planarity : 0.006 0.064 3952 Dihedral : 5.530 53.334 3261 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.73 % Favored : 89.20 % Rotamer: Outliers : 6.21 % Allowed : 27.88 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.19 (0.16), residues: 2936 helix: 0.67 (0.13), residues: 1569 sheet: -1.32 (0.31), residues: 263 loop : -2.90 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 21 HIS 0.004 0.001 HIS J 266 PHE 0.012 0.001 PHE C 204 TYR 0.018 0.002 TYR G 96 ARG 0.008 0.000 ARG J 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 317 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 138 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8455 (tt) REVERT: B 264 TRP cc_start: 0.6893 (m-90) cc_final: 0.6152 (m-10) REVERT: B 449 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7113 (t80) REVERT: C 204 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7683 (t80) REVERT: C 277 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7705 (mm) REVERT: C 411 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7005 (tp) REVERT: F 231 TRP cc_start: 0.8071 (p90) cc_final: 0.7561 (p90) REVERT: F 397 LEU cc_start: 0.8757 (pp) cc_final: 0.8439 (tp) REVERT: G 200 LYS cc_start: 0.8567 (tppt) cc_final: 0.8289 (mmmt) REVERT: E 132 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7367 (mt) REVERT: E 432 LYS cc_start: 0.7958 (tttt) cc_final: 0.7622 (mmtm) REVERT: I 45 MET cc_start: 0.7694 (tpt) cc_final: 0.7376 (tmm) REVERT: D 96 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7932 (t80) outliers start: 143 outliers final: 112 residues processed: 415 average time/residue: 0.2919 time to fit residues: 198.9779 Evaluate side-chains 423 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 303 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN G 74 HIS H 331 GLN J 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22871 Z= 0.201 Angle : 0.729 15.163 31317 Z= 0.348 Chirality : 0.042 0.231 3896 Planarity : 0.005 0.062 3952 Dihedral : 5.216 54.376 3259 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.40 % Favored : 90.53 % Rotamer: Outliers : 4.73 % Allowed : 29.70 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.90 (0.16), residues: 2936 helix: 0.95 (0.14), residues: 1559 sheet: -1.13 (0.32), residues: 270 loop : -2.82 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 164 HIS 0.005 0.001 HIS J 266 PHE 0.015 0.001 PHE E 469 TYR 0.014 0.001 TYR G 96 ARG 0.007 0.000 ARG J 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 345 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8314 (tt) REVERT: B 264 TRP cc_start: 0.6928 (m-90) cc_final: 0.6230 (m-10) REVERT: B 449 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7008 (t80) REVERT: C 204 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7692 (t80) REVERT: C 277 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7732 (mm) REVERT: C 411 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.6900 (tp) REVERT: F 144 ARG cc_start: 0.7062 (mtp180) cc_final: 0.6409 (mtt180) REVERT: F 231 TRP cc_start: 0.8025 (p90) cc_final: 0.7545 (p90) REVERT: F 357 ARG cc_start: 0.6457 (mtt180) cc_final: 0.6242 (mtt180) REVERT: F 397 LEU cc_start: 0.8691 (pp) cc_final: 0.8385 (tp) REVERT: G 200 LYS cc_start: 0.8549 (tppt) cc_final: 0.8213 (mmmt) REVERT: E 432 LYS cc_start: 0.7929 (tttt) cc_final: 0.7599 (mmtm) REVERT: J 364 ASP cc_start: 0.7563 (p0) cc_final: 0.7141 (p0) REVERT: D 96 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7831 (t80) outliers start: 109 outliers final: 85 residues processed: 412 average time/residue: 0.3085 time to fit residues: 210.5960 Evaluate side-chains 417 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 326 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 0.8980 chunk 283 optimal weight: 9.9990 chunk 172 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 296 optimal weight: 0.3980 chunk 273 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** F 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS H 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22871 Z= 0.211 Angle : 0.740 16.180 31317 Z= 0.354 Chirality : 0.042 0.219 3896 Planarity : 0.005 0.062 3952 Dihedral : 5.126 54.458 3258 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.88 % Favored : 90.05 % Rotamer: Outliers : 4.21 % Allowed : 30.35 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.16), residues: 2936 helix: 0.99 (0.14), residues: 1561 sheet: -1.12 (0.32), residues: 259 loop : -2.76 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 164 HIS 0.004 0.001 HIS C 154 PHE 0.024 0.001 PHE F 6 TYR 0.020 0.002 TYR E 407 ARG 0.006 0.000 ARG J 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 329 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 TRP cc_start: 0.6913 (m-90) cc_final: 0.6220 (m-10) REVERT: B 449 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7085 (t80) REVERT: C 204 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7721 (t80) REVERT: C 277 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7745 (mm) REVERT: C 411 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.6918 (tp) REVERT: F 144 ARG cc_start: 0.7062 (mtp180) cc_final: 0.6441 (mtt180) REVERT: F 357 ARG cc_start: 0.6463 (mtt180) cc_final: 0.6258 (mtt180) REVERT: F 397 LEU cc_start: 0.8701 (pp) cc_final: 0.8395 (tp) REVERT: G 200 LYS cc_start: 0.8563 (tppt) cc_final: 0.8215 (mmmt) REVERT: E 432 LYS cc_start: 0.7913 (tttt) cc_final: 0.7598 (mmtm) REVERT: J 364 ASP cc_start: 0.7564 (p0) cc_final: 0.7138 (p0) REVERT: D 96 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7832 (t80) outliers start: 97 outliers final: 84 residues processed: 390 average time/residue: 0.2791 time to fit residues: 179.5445 Evaluate side-chains 412 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 323 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 0.0870 chunk 251 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 236 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** F 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.134443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.112005 restraints weight = 68328.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112845 restraints weight = 39800.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.113331 restraints weight = 31347.727| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22871 Z= 0.257 Angle : 0.753 15.993 31317 Z= 0.363 Chirality : 0.043 0.239 3896 Planarity : 0.005 0.063 3952 Dihedral : 5.209 52.988 3258 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.15 % Favored : 89.78 % Rotamer: Outliers : 4.52 % Allowed : 30.05 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.16), residues: 2936 helix: 0.96 (0.14), residues: 1557 sheet: -1.14 (0.32), residues: 268 loop : -2.74 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 164 HIS 0.004 0.001 HIS C 154 PHE 0.021 0.001 PHE F 6 TYR 0.019 0.002 TYR E 407 ARG 0.006 0.000 ARG H 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4784.00 seconds wall clock time: 87 minutes 20.89 seconds (5240.89 seconds total)