Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 07:58:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/04_2023/6lar_0862.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/04_2023/6lar_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_0862/04_2023/6lar_0862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/04_2023/6lar_0862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/04_2023/6lar_0862.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lar_0862/04_2023/6lar_0862.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 11.61, per 1000 atoms: 0.52 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: 9.00 Conformation dependent library (CDL) restraints added in 3.6 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: 1.04 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: 6.91 Time building geometry restraints manager: 9.62 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: 6.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 19.220 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 55.690 Find NCS groups from input model: 1.530 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.700 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.575 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 outliers start: 126 outliers final: 51 residues processed: 557 average time/residue: 0.3704 time to fit residues: 307.5826 Evaluate side-chains 366 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 315 time to evaluate : 2.509 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2207 time to fit residues: 23.5201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 1.9990 chunk 225 optimal weight: 0.0170 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 233 optimal weight: 0.1980 chunk 90 optimal weight: 0.0870 chunk 142 optimal weight: 0.0870 chunk 173 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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: 0.7491 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 22871 Z= 0.220 Angle : 0.766 8.944 31317 Z= 0.376 Chirality : 0.044 0.280 3896 Planarity : 0.006 0.058 3952 Dihedral : 5.254 28.192 3244 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.60 % Favored : 90.33 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.81 (0.15), residues: 2936 helix: -0.76 (0.13), residues: 1599 sheet: -1.93 (0.29), residues: 273 loop : -3.56 (0.17), residues: 1064 *********************** 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 484 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 418 time to evaluate : 2.641 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 outliers start: 66 outliers final: 37 residues processed: 452 average time/residue: 0.3283 time to fit residues: 233.0585 Evaluate side-chains 360 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 323 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1920 time to fit residues: 17.0145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.0470 chunk 83 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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** G 22 GLN E 126 GLN ** H 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7509 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22871 Z= 0.203 Angle : 0.709 11.512 31317 Z= 0.344 Chirality : 0.042 0.298 3896 Planarity : 0.005 0.056 3952 Dihedral : 4.918 27.550 3244 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.81 % Favored : 90.12 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.94 (0.15), residues: 2936 helix: 0.10 (0.13), residues: 1577 sheet: -1.81 (0.30), residues: 269 loop : -3.29 (0.17), residues: 1090 *********************** 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 421 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 360 time to evaluate : 2.332 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 outliers start: 61 outliers final: 28 residues processed: 396 average time/residue: 0.3320 time to fit residues: 211.7943 Evaluate side-chains 340 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 312 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2084 time to fit residues: 14.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 0.2980 chunk 203 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 272 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 257 optimal weight: 7.9990 chunk 77 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN G 22 GLN ** H 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7473 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 22871 Z= 0.182 Angle : 0.686 13.396 31317 Z= 0.329 Chirality : 0.042 0.293 3896 Planarity : 0.005 0.052 3952 Dihedral : 4.672 26.677 3244 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.89 % Favored : 91.04 % Rotamer Outliers : 2.30 % 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: -1.50 (0.16), residues: 2936 helix: 0.45 (0.14), residues: 1595 sheet: -1.66 (0.30), residues: 275 loop : -3.12 (0.18), residues: 1066 *********************** 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 419 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 366 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 19 residues processed: 403 average time/residue: 0.2999 time to fit residues: 196.7207 Evaluate side-chains 344 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 325 time to evaluate : 2.577 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1985 time to fit residues: 10.4769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 245 optimal weight: 0.0470 chunk 199 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- 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 389 HIS G 63 ASN H 154 HIS ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 22871 Z= 0.242 Angle : 0.713 13.560 31317 Z= 0.346 Chirality : 0.043 0.281 3896 Planarity : 0.005 0.055 3952 Dihedral : 4.721 26.577 3244 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.60 % Favored : 90.33 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.38 (0.16), residues: 2936 helix: 0.48 (0.13), residues: 1599 sheet: -1.43 (0.30), residues: 283 loop : -3.02 (0.18), residues: 1054 *********************** 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 396 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 330 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 40 residues processed: 379 average time/residue: 0.3181 time to fit residues: 193.6600 Evaluate side-chains 344 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 304 time to evaluate : 2.542 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1973 time to fit residues: 18.6364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 169 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** E 126 GLN E 330 HIS H 126 GLN ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 22871 Z= 0.203 Angle : 0.697 15.007 31317 Z= 0.335 Chirality : 0.042 0.318 3896 Planarity : 0.005 0.055 3952 Dihedral : 4.627 27.752 3244 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.26 % Favored : 90.67 % Rotamer Outliers : 2.00 % 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: -1.15 (0.16), residues: 2936 helix: 0.67 (0.14), residues: 1595 sheet: -1.25 (0.30), residues: 283 loop : -2.94 (0.18), residues: 1058 *********************** 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 389 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 343 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 371 average time/residue: 0.3003 time to fit residues: 183.1365 Evaluate side-chains 332 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 313 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2117 time to fit residues: 10.9023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 210 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** E 331 GLN ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 22871 Z= 0.242 Angle : 0.715 14.572 31317 Z= 0.346 Chirality : 0.043 0.303 3896 Planarity : 0.005 0.059 3952 Dihedral : 4.673 29.554 3244 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.95 % Favored : 89.99 % Rotamer Outliers : 1.74 % 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: -1.11 (0.16), residues: 2936 helix: 0.66 (0.13), residues: 1598 sheet: -1.16 (0.31), residues: 271 loop : -2.85 (0.19), residues: 1067 *********************** 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 356 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 316 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 340 average time/residue: 0.3039 time to fit residues: 168.2166 Evaluate side-chains 321 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2034 time to fit residues: 11.2265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 171 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 195 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 225 optimal weight: 0.4980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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** E 331 GLN H 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 22871 Z= 0.180 Angle : 0.690 15.058 31317 Z= 0.330 Chirality : 0.041 0.283 3896 Planarity : 0.005 0.056 3952 Dihedral : 4.451 28.700 3244 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.31 % Favored : 91.62 % Rotamer Outliers : 0.83 % 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: -0.79 (0.16), residues: 2936 helix: 0.95 (0.14), residues: 1594 sheet: -1.05 (0.31), residues: 283 loop : -2.76 (0.19), residues: 1059 *********************** 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 360 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 341 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 353 average time/residue: 0.3076 time to fit residues: 178.9997 Evaluate side-chains 321 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 312 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2139 time to fit residues: 6.7958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 241 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** B 126 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** H 331 GLN J 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 22871 Z= 0.194 Angle : 0.714 15.582 31317 Z= 0.342 Chirality : 0.042 0.335 3896 Planarity : 0.005 0.056 3952 Dihedral : 4.407 31.277 3244 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.79 % Favored : 91.14 % Rotamer Outliers : 0.74 % 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: -0.75 (0.16), residues: 2936 helix: 0.95 (0.14), residues: 1593 sheet: -0.89 (0.32), residues: 276 loop : -2.70 (0.19), residues: 1067 *********************** 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 347 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 330 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 340 average time/residue: 0.3124 time to fit residues: 175.6273 Evaluate side-chains 324 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 312 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2041 time to fit residues: 8.3325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 0.0270 chunk 283 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 chunk 196 optimal weight: 9.9990 chunk 296 optimal weight: 0.0970 chunk 273 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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** H 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 22871 Z= 0.181 Angle : 0.706 15.494 31317 Z= 0.337 Chirality : 0.042 0.312 3896 Planarity : 0.005 0.061 3952 Dihedral : 4.304 29.630 3244 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.45 % Favored : 91.49 % Rotamer Outliers : 0.56 % 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: -0.61 (0.16), residues: 2936 helix: 1.06 (0.14), residues: 1590 sheet: -0.80 (0.32), residues: 290 loop : -2.68 (0.19), residues: 1056 ********************** 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 350 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 337 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 347 average time/residue: 0.2998 time to fit residues: 169.9560 Evaluate side-chains 320 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 313 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2011 time to fit residues: 6.2572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 7.9990 chunk 251 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 236 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 216 ASN F 130 HIS H 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.139146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.118199 restraints weight = 68387.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.118156 restraints weight = 49517.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118663 restraints weight = 50632.259| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22871 Z= 0.196 Angle : 0.715 15.683 31317 Z= 0.340 Chirality : 0.042 0.296 3896 Planarity : 0.005 0.056 3952 Dihedral : 4.293 24.000 3244 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.65 % Favored : 91.31 % Rotamer Outliers : 0.22 % 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: -0.58 (0.16), residues: 2936 helix: 1.10 (0.14), residues: 1587 sheet: -0.72 (0.33), residues: 276 loop : -2.65 (0.19), residues: 1073 =============================================================================== Job complete usr+sys time: 4519.73 seconds wall clock time: 83 minutes 13.30 seconds (4993.30 seconds total)