Starting phenix.real_space_refine on Wed Jun 18 14:10:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y0d_33540/06_2025/7y0d_33540.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0d_33540/06_2025/7y0d_33540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y0d_33540/06_2025/7y0d_33540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0d_33540/06_2025/7y0d_33540.map" model { file = "/net/cci-nas-00/data/ceres_data/7y0d_33540/06_2025/7y0d_33540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0d_33540/06_2025/7y0d_33540.cif" } resolution = 3.1 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= 0.002 sd= 0.124 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 64 5.16 5 C 13136 2.51 5 N 3824 2.21 5 O 4200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21224 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "B" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "C" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "E" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "F" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "G" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "H" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Time building chain proxies: 13.32, per 1000 atoms: 0.63 Number of scatterers: 21224 At special positions: 0 Unit cell: (110.21, 112.35, 201.16, 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 64 16.00 O 4200 8.00 N 3824 7.00 C 13136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.8 seconds 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 20 sheets defined 66.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 5.182A pdb=" N GLY A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 73 through 81 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 155 through 189 removed outlier: 3.522A pdb=" N ILE A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.898A pdb=" N ARG A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.543A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.942A pdb=" N GLN A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 329 through 335 removed outlier: 4.027A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.943A pdb=" N LEU A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 361 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 20 through 28 removed outlier: 4.952A pdb=" N GLY B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 44 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.756A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 78 " --> pdb=" O PRO B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 145 through 149 removed outlier: 4.027A pdb=" N GLY B 148 " --> pdb=" O TYR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 190 removed outlier: 3.516A pdb=" N GLU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 223 removed outlier: 3.906A pdb=" N VAL B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 239 through 251 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.715A pdb=" N PHE B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.726A pdb=" N VAL B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.515A pdb=" N ALA B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 358 " --> pdb=" O HIS B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.649A pdb=" N THR C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 44 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 73 through 81 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 155 through 190 removed outlier: 3.651A pdb=" N ALA C 168 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 223 removed outlier: 4.294A pdb=" N VAL C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 207 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.649A pdb=" N GLY C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 251 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 280 through 289 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.613A pdb=" N MET C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.704A pdb=" N LEU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 removed outlier: 3.680A pdb=" N VAL C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 363 removed outlier: 3.662A pdb=" N GLY C 358 " --> pdb=" O HIS C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 removed outlier: 4.947A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 55 through 62 Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 145 through 149 removed outlier: 4.050A pdb=" N GLY D 148 " --> pdb=" O TYR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 190 removed outlier: 3.706A pdb=" N ILE D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 223 removed outlier: 4.473A pdb=" N VAL D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 202 " --> pdb=" O VAL D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 280 through 289 Processing helix chain 'D' and resid 293 through 297 removed outlier: 3.891A pdb=" N GLN D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 339 through 344 Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.813A pdb=" N ILE D 355 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 363 " --> pdb=" O LEU D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 28 removed outlier: 5.367A pdb=" N GLY E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 44 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 73 through 81 removed outlier: 3.615A pdb=" N LEU E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 116 through 128 Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 155 through 190 removed outlier: 4.040A pdb=" N ALA E 168 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 223 removed outlier: 3.518A pdb=" N VAL E 198 " --> pdb=" O THR E 194 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 239 through 251 Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 289 removed outlier: 3.650A pdb=" N LEU E 284 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 316 through 328 Processing helix chain 'E' and resid 329 through 335 removed outlier: 3.746A pdb=" N LEU E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 344 removed outlier: 3.593A pdb=" N SER E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL E 344 " --> pdb=" O ASP E 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 339 through 344' Processing helix chain 'E' and resid 349 through 364 removed outlier: 4.391A pdb=" N GLU E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 removed outlier: 5.257A pdb=" N GLY F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 44 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 115 through 128 removed outlier: 3.662A pdb=" N GLU F 122 " --> pdb=" O HIS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 removed outlier: 4.201A pdb=" N GLY F 148 " --> pdb=" O TYR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 189 removed outlier: 3.531A pdb=" N ILE F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 223 removed outlier: 4.142A pdb=" N VAL F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL F 202 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET F 207 " --> pdb=" O GLN F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 237 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.776A pdb=" N LEU F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 279 Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.545A pdb=" N LEU F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.580A pdb=" N ASP F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 311 removed outlier: 4.053A pdb=" N ALA F 311 " --> pdb=" O ARG F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 328 Processing helix chain 'F' and resid 329 through 336 Processing helix chain 'F' and resid 337 through 344 Processing helix chain 'F' and resid 348 through 364 Processing helix chain 'G' and resid 20 through 28 removed outlier: 5.567A pdb=" N GLY G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 44 Processing helix chain 'G' and resid 55 through 62 Processing helix chain 'G' and resid 73 through 81 removed outlier: 4.427A pdb=" N LEU G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG G 78 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 115 through 128 Processing helix chain 'G' and resid 145 through 149 removed outlier: 4.190A pdb=" N GLY G 148 " --> pdb=" O TYR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 190 removed outlier: 3.603A pdb=" N ILE G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR G 169 " --> pdb=" O GLN G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 223 removed outlier: 4.081A pdb=" N VAL G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL G 202 " --> pdb=" O VAL G 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 238 removed outlier: 3.596A pdb=" N GLY G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 251 Processing helix chain 'G' and resid 259 through 272 Processing helix chain 'G' and resid 274 through 279 Processing helix chain 'G' and resid 280 through 289 removed outlier: 3.613A pdb=" N PHE G 288 " --> pdb=" O LEU G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 299 Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 329 through 335 removed outlier: 3.900A pdb=" N LEU G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 344 Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.579A pdb=" N GLY G 358 " --> pdb=" O HIS G 354 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU G 364 " --> pdb=" O SER G 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 28 removed outlier: 5.340A pdb=" N GLY H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 44 Processing helix chain 'H' and resid 55 through 62 Processing helix chain 'H' and resid 73 through 81 Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 115 through 128 Processing helix chain 'H' and resid 155 through 189 removed outlier: 3.714A pdb=" N ALA H 168 " --> pdb=" O ASN H 164 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR H 169 " --> pdb=" O GLN H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 223 removed outlier: 4.154A pdb=" N VAL H 201 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL H 202 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 238 Processing helix chain 'H' and resid 240 through 251 Processing helix chain 'H' and resid 259 through 273 Processing helix chain 'H' and resid 280 through 289 removed outlier: 3.641A pdb=" N LEU H 284 " --> pdb=" O ASP H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 316 through 328 Processing helix chain 'H' and resid 329 through 335 removed outlier: 3.535A pdb=" N LEU H 333 " --> pdb=" O SER H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 344 Processing helix chain 'H' and resid 348 through 363 removed outlier: 3.501A pdb=" N ARG H 353 " --> pdb=" O SER H 349 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY H 358 " --> pdb=" O HIS H 354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 71 removed outlier: 6.471A pdb=" N LEU A 97 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 70 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG A 95 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL A 142 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 194 removed outlier: 3.675A pdb=" N VAL A 193 " --> pdb=" O MET A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63 removed outlier: 5.287A pdb=" N ALA B 99 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 88 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'C' and resid 66 through 71 removed outlier: 6.651A pdb=" N LEU C 97 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 70 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG C 95 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 98 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 49 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU C 89 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 51 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 132 " --> pdb=" O TYR C 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.597A pdb=" N ASP C 63 " --> pdb=" O GLN C 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'D' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'D' and resid 142 through 144 removed outlier: 4.552A pdb=" N VAL D 142 " --> pdb=" O VAL D 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 87 through 89 removed outlier: 3.839A pdb=" N VAL E 132 " --> pdb=" O TYR E 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 62 through 63 removed outlier: 4.056A pdb=" N ASP E 63 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'F' and resid 62 through 63 removed outlier: 3.565A pdb=" N VAL F 70 " --> pdb=" O ILE F 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 62 through 63 removed outlier: 5.642A pdb=" N ALA F 99 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL F 88 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 49 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU F 89 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL F 51 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 142 through 144 removed outlier: 4.645A pdb=" N VAL F 142 " --> pdb=" O VAL F 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 87 through 89 removed outlier: 6.291A pdb=" N LEU G 49 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU G 89 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL G 51 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 135 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL G 142 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AC1, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.665A pdb=" N LEU H 97 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL H 70 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG H 95 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA H 86 " --> pdb=" O ASN H 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 145 through 146 removed outlier: 3.612A pdb=" N VAL H 146 " --> pdb=" O GLU H 149 " (cutoff:3.500A) 1262 hydrogen bonds defined for protein. 3645 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: 7.52 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7500 1.34 - 1.46: 2932 1.46 - 1.58: 10952 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 21504 Sorted by residual: bond pdb=" CB PRO H 110 " pdb=" CG PRO H 110 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.13e+00 bond pdb=" CA MET D 83 " pdb=" C MET D 83 " ideal model delta sigma weight residual 1.518 1.575 -0.058 4.01e-02 6.22e+02 2.06e+00 bond pdb=" CG GLU E 268 " pdb=" CD GLU E 268 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.72e+00 bond pdb=" CG GLU B 171 " pdb=" CD GLU B 171 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" CA ILE F 96 " pdb=" CB ILE F 96 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.42e+00 ... (remaining 21499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 28637 1.92 - 3.84: 458 3.84 - 5.77: 78 5.77 - 7.69: 16 7.69 - 9.61: 3 Bond angle restraints: 29192 Sorted by residual: angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" CB GLU B 171 " ideal model delta sigma weight residual 110.39 117.15 -6.76 1.66e+00 3.63e-01 1.66e+01 angle pdb=" N GLU E 268 " pdb=" CA GLU E 268 " pdb=" CB GLU E 268 " ideal model delta sigma weight residual 110.28 116.29 -6.01 1.55e+00 4.16e-01 1.51e+01 angle pdb=" N VAL G 104 " pdb=" CA VAL G 104 " pdb=" C VAL G 104 " ideal model delta sigma weight residual 107.55 111.28 -3.73 9.90e-01 1.02e+00 1.42e+01 angle pdb=" N ASP B 191 " pdb=" CA ASP B 191 " pdb=" C ASP B 191 " ideal model delta sigma weight residual 110.64 116.06 -5.42 1.48e+00 4.57e-01 1.34e+01 angle pdb=" N ASP A 191 " pdb=" CA ASP A 191 " pdb=" C ASP A 191 " ideal model delta sigma weight residual 110.64 116.01 -5.37 1.48e+00 4.57e-01 1.32e+01 ... (remaining 29187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11889 17.81 - 35.62: 1168 35.62 - 53.43: 150 53.43 - 71.25: 28 71.25 - 89.06: 13 Dihedral angle restraints: 13248 sinusoidal: 5256 harmonic: 7992 Sorted by residual: dihedral pdb=" CA GLU H 190 " pdb=" C GLU H 190 " pdb=" N ASP H 191 " pdb=" CA ASP H 191 " ideal model delta harmonic sigma weight residual 180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ARG E 22 " pdb=" C ARG E 22 " pdb=" N GLU E 23 " pdb=" CA GLU E 23 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA GLU B 190 " pdb=" C GLU B 190 " pdb=" N ASP B 191 " pdb=" CA ASP B 191 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 13245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2271 0.032 - 0.064: 822 0.064 - 0.095: 246 0.095 - 0.127: 135 0.127 - 0.159: 14 Chirality restraints: 3488 Sorted by residual: chirality pdb=" CA MET D 199 " pdb=" N MET D 199 " pdb=" C MET D 199 " pdb=" CB MET D 199 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB ILE F 189 " pdb=" CA ILE F 189 " pdb=" CG1 ILE F 189 " pdb=" CG2 ILE F 189 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA LEU H 97 " pdb=" N LEU H 97 " pdb=" C LEU H 97 " pdb=" CB LEU H 97 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.26e-01 ... (remaining 3485 not shown) Planarity restraints: 3840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 104 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO H 105 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 105 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 105 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 254 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO D 255 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 29 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO H 30 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 30 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 30 " 0.026 5.00e-02 4.00e+02 ... (remaining 3837 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 647 2.71 - 3.25: 23206 3.25 - 3.80: 35388 3.80 - 4.35: 42519 4.35 - 4.90: 70312 Nonbonded interactions: 172072 Sorted by model distance: nonbonded pdb=" OE2 GLU C 188 " pdb=" OH TYR C 251 " model vdw 2.158 3.040 nonbonded pdb=" OG SER D 156 " pdb=" OD2 ASP D 225 " model vdw 2.177 3.040 nonbonded pdb=" OE2 GLU E 188 " pdb=" OH TYR E 251 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR B 111 " pdb=" OE1 GLU B 122 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASP G 250 " pdb=" OG SER G 303 " model vdw 2.218 3.040 ... (remaining 172067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 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: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 49.270 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 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: 59.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.003 0.073 21504 Z= 0.147 Angle : 0.606 9.611 29192 Z= 0.310 Chirality : 0.041 0.159 3488 Planarity : 0.004 0.060 3840 Dihedral : 13.787 89.057 8080 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.77 (0.16), residues: 2752 helix: 1.16 (0.13), residues: 1568 sheet: -0.58 (0.64), residues: 80 loop : -0.24 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 351 HIS 0.003 0.001 HIS G 354 PHE 0.026 0.001 PHE A 192 TYR 0.023 0.001 TYR B 173 ARG 0.012 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.16399 ( 1260) hydrogen bonds : angle 5.84283 ( 3645) covalent geometry : bond 0.00335 (21504) covalent geometry : angle 0.60582 (29192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 199 MET cc_start: 0.8294 (ttm) cc_final: 0.7850 (ttm) REVERT: B 301 MET cc_start: 0.7609 (pmm) cc_final: 0.7254 (pmm) REVERT: D 61 ILE cc_start: 0.5328 (mm) cc_final: 0.4625 (tt) REVERT: D 77 LEU cc_start: 0.8084 (pt) cc_final: 0.7851 (pt) REVERT: H 139 MET cc_start: 0.6836 (mmm) cc_final: 0.6597 (mtp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2873 time to fit residues: 80.6070 Evaluate side-chains 120 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 319 HIS B 127 GLN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 HIS G 232 GLN G 319 HIS ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.132417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.098075 restraints weight = 63200.665| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.95 r_work: 0.3675 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21504 Z= 0.200 Angle : 0.667 12.300 29192 Z= 0.335 Chirality : 0.042 0.169 3488 Planarity : 0.005 0.051 3840 Dihedral : 4.731 31.043 3088 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.86 % Allowed : 8.71 % Favored : 90.43 % 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: 0.50 (0.16), residues: 2752 helix: 0.97 (0.13), residues: 1624 sheet: -1.14 (0.60), residues: 80 loop : -0.45 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 351 HIS 0.008 0.001 HIS H 252 PHE 0.016 0.002 PHE A 192 TYR 0.021 0.002 TYR E 54 ARG 0.006 0.001 ARG G 40 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1260) hydrogen bonds : angle 4.65395 ( 3645) covalent geometry : bond 0.00455 (21504) covalent geometry : angle 0.66707 (29192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6937 (t80) cc_final: 0.6477 (t80) REVERT: B 54 TYR cc_start: 0.7058 (t80) cc_final: 0.6337 (t80) REVERT: B 199 MET cc_start: 0.7806 (ttm) cc_final: 0.7540 (ttm) REVERT: B 309 MET cc_start: 0.8692 (ppp) cc_final: 0.8244 (ppp) REVERT: D 61 ILE cc_start: 0.5541 (mm) cc_final: 0.4481 (tt) REVERT: F 284 LEU cc_start: 0.9160 (tt) cc_final: 0.8730 (mt) REVERT: H 221 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7787 (mt-10) outliers start: 20 outliers final: 14 residues processed: 151 average time/residue: 0.2694 time to fit residues: 69.6717 Evaluate side-chains 138 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 234 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 262 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.134709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.099907 restraints weight = 60783.696| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.88 r_work: 0.3682 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21504 Z= 0.177 Angle : 0.640 14.025 29192 Z= 0.316 Chirality : 0.041 0.234 3488 Planarity : 0.005 0.049 3840 Dihedral : 4.627 30.419 3088 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.42 % Allowed : 11.77 % Favored : 86.81 % 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: 0.46 (0.16), residues: 2752 helix: 1.00 (0.13), residues: 1640 sheet: -1.34 (0.59), residues: 80 loop : -0.57 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 351 HIS 0.005 0.001 HIS H 252 PHE 0.013 0.001 PHE A 192 TYR 0.041 0.002 TYR F 173 ARG 0.005 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 1260) hydrogen bonds : angle 4.43486 ( 3645) covalent geometry : bond 0.00404 (21504) covalent geometry : angle 0.63984 (29192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7161 (t80) cc_final: 0.6856 (t80) REVERT: A 309 MET cc_start: 0.8048 (ppp) cc_final: 0.7443 (ppp) REVERT: B 165 GLN cc_start: 0.9223 (mp10) cc_final: 0.9014 (mp10) REVERT: B 309 MET cc_start: 0.8699 (ppp) cc_final: 0.8395 (ppp) REVERT: C 288 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7239 (m-10) REVERT: C 350 MET cc_start: 0.8553 (tmm) cc_final: 0.8306 (tpt) REVERT: D 61 ILE cc_start: 0.5633 (mm) cc_final: 0.4577 (tt) REVERT: D 199 MET cc_start: 0.6498 (mtm) cc_final: 0.6083 (mtt) REVERT: D 290 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6564 (m-10) REVERT: E 199 MET cc_start: -0.0441 (mmt) cc_final: -0.0645 (mmt) REVERT: G 199 MET cc_start: 0.6677 (ttp) cc_final: 0.6433 (ttp) REVERT: G 207 MET cc_start: 0.8071 (ttm) cc_final: 0.7726 (mtp) REVERT: H 221 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7806 (mt-10) outliers start: 33 outliers final: 18 residues processed: 161 average time/residue: 0.2869 time to fit residues: 76.5074 Evaluate side-chains 146 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 234 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 188 optimal weight: 4.9990 chunk 164 optimal weight: 0.0020 chunk 155 optimal weight: 0.8980 chunk 270 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS B 165 GLN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.134613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.099530 restraints weight = 61659.710| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 4.13 r_work: 0.3675 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21504 Z= 0.171 Angle : 0.629 12.722 29192 Z= 0.310 Chirality : 0.041 0.283 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.593 30.867 3088 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.85 % Allowed : 13.84 % Favored : 84.31 % 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: 0.45 (0.16), residues: 2752 helix: 0.96 (0.13), residues: 1688 sheet: -1.46 (0.59), residues: 80 loop : -0.58 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 351 HIS 0.005 0.001 HIS A 319 PHE 0.014 0.001 PHE F 288 TYR 0.024 0.002 TYR F 173 ARG 0.004 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 1260) hydrogen bonds : angle 4.32293 ( 3645) covalent geometry : bond 0.00391 (21504) covalent geometry : angle 0.62872 (29192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7128 (t80) cc_final: 0.6821 (t80) REVERT: C 288 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: D 61 ILE cc_start: 0.5580 (mm) cc_final: 0.4569 (tt) REVERT: D 290 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6644 (m-10) REVERT: E 199 MET cc_start: -0.0499 (mmt) cc_final: -0.0715 (mmt) REVERT: G 207 MET cc_start: 0.8161 (ttm) cc_final: 0.7740 (mtp) REVERT: H 221 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7826 (mt-10) REVERT: H 278 LEU cc_start: 0.8733 (mt) cc_final: 0.8179 (mt) outliers start: 43 outliers final: 29 residues processed: 171 average time/residue: 0.3019 time to fit residues: 87.2656 Evaluate side-chains 157 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 270 optimal weight: 9.9990 chunk 262 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.131034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.096079 restraints weight = 64113.090| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.80 r_work: 0.3658 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21504 Z= 0.226 Angle : 0.682 12.876 29192 Z= 0.339 Chirality : 0.043 0.256 3488 Planarity : 0.005 0.055 3840 Dihedral : 4.825 33.694 3088 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.46 % Allowed : 15.39 % Favored : 82.16 % 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: 0.36 (0.16), residues: 2752 helix: 0.89 (0.13), residues: 1672 sheet: -1.71 (0.59), residues: 80 loop : -0.57 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 351 HIS 0.006 0.001 HIS A 319 PHE 0.011 0.001 PHE G 288 TYR 0.019 0.002 TYR F 173 ARG 0.005 0.000 ARG D 150 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 1260) hydrogen bonds : angle 4.41196 ( 3645) covalent geometry : bond 0.00518 (21504) covalent geometry : angle 0.68152 (29192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7822 (ppp) cc_final: 0.7184 (ppp) REVERT: B 309 MET cc_start: 0.8846 (ppp) cc_final: 0.8504 (ppp) REVERT: C 288 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7370 (m-10) REVERT: D 61 ILE cc_start: 0.5672 (mm) cc_final: 0.4707 (tt) REVERT: D 290 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6689 (m-10) REVERT: E 199 MET cc_start: -0.0504 (mmt) cc_final: -0.0716 (mmt) REVERT: F 139 MET cc_start: 0.7631 (mmm) cc_final: 0.7388 (mmm) REVERT: F 267 LEU cc_start: 0.9255 (mt) cc_final: 0.9010 (pp) REVERT: G 45 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8147 (mtm110) REVERT: G 207 MET cc_start: 0.8188 (ttm) cc_final: 0.7826 (mtp) REVERT: H 221 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7850 (mt-10) REVERT: H 278 LEU cc_start: 0.8750 (mt) cc_final: 0.8172 (mt) outliers start: 57 outliers final: 37 residues processed: 178 average time/residue: 0.2701 time to fit residues: 79.5280 Evaluate side-chains 162 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 92 optimal weight: 0.9990 chunk 134 optimal weight: 0.0060 chunk 100 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.131943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097665 restraints weight = 64053.218| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.81 r_work: 0.3693 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21504 Z= 0.147 Angle : 0.633 14.748 29192 Z= 0.310 Chirality : 0.041 0.257 3488 Planarity : 0.004 0.051 3840 Dihedral : 4.593 31.778 3088 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.33 % Allowed : 16.59 % Favored : 81.08 % 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: 0.49 (0.16), residues: 2752 helix: 1.00 (0.13), residues: 1680 sheet: -1.56 (0.60), residues: 80 loop : -0.56 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 351 HIS 0.015 0.001 HIS A 319 PHE 0.011 0.001 PHE G 288 TYR 0.043 0.001 TYR F 173 ARG 0.008 0.000 ARG G 353 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 1260) hydrogen bonds : angle 4.25126 ( 3645) covalent geometry : bond 0.00338 (21504) covalent geometry : angle 0.63296 (29192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6666 (t80) cc_final: 0.6394 (t80) REVERT: A 309 MET cc_start: 0.7768 (ppp) cc_final: 0.7195 (ppp) REVERT: B 309 MET cc_start: 0.8927 (ppp) cc_final: 0.8631 (ppp) REVERT: C 288 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: D 61 ILE cc_start: 0.5565 (mm) cc_final: 0.4727 (tt) REVERT: D 279 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7834 (pp) REVERT: D 290 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6671 (m-10) REVERT: E 199 MET cc_start: -0.0642 (mmt) cc_final: -0.0873 (mmt) REVERT: F 139 MET cc_start: 0.7644 (mmm) cc_final: 0.7402 (mmm) REVERT: F 267 LEU cc_start: 0.9254 (mt) cc_final: 0.8979 (pp) REVERT: G 45 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8158 (mtm110) REVERT: G 207 MET cc_start: 0.8158 (ttm) cc_final: 0.7737 (mtp) REVERT: G 278 LEU cc_start: 0.8490 (tp) cc_final: 0.8157 (tt) REVERT: G 339 ASP cc_start: 0.9699 (t0) cc_final: 0.9247 (p0) REVERT: H 221 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7950 (mt-10) REVERT: H 278 LEU cc_start: 0.8746 (mt) cc_final: 0.8173 (mt) outliers start: 54 outliers final: 29 residues processed: 178 average time/residue: 0.3407 time to fit residues: 102.4118 Evaluate side-chains 158 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 192 optimal weight: 6.9990 chunk 109 optimal weight: 0.0270 chunk 68 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 267 optimal weight: 0.0870 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.132179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.097904 restraints weight = 63784.202| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.81 r_work: 0.3697 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21504 Z= 0.145 Angle : 0.629 12.538 29192 Z= 0.309 Chirality : 0.041 0.175 3488 Planarity : 0.004 0.051 3840 Dihedral : 4.518 31.232 3088 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.46 % Allowed : 16.85 % Favored : 80.69 % 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: 0.55 (0.16), residues: 2752 helix: 1.05 (0.13), residues: 1680 sheet: -1.52 (0.60), residues: 80 loop : -0.54 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 351 HIS 0.009 0.001 HIS B 354 PHE 0.016 0.001 PHE F 281 TYR 0.046 0.001 TYR F 173 ARG 0.005 0.000 ARG F 172 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 1260) hydrogen bonds : angle 4.18711 ( 3645) covalent geometry : bond 0.00333 (21504) covalent geometry : angle 0.62933 (29192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7839 (ppp) cc_final: 0.7307 (ppp) REVERT: B 309 MET cc_start: 0.9005 (ppp) cc_final: 0.8746 (ppp) REVERT: C 207 MET cc_start: 0.7878 (ptp) cc_final: 0.7391 (pmm) REVERT: C 288 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7354 (m-10) REVERT: D 61 ILE cc_start: 0.5573 (mm) cc_final: 0.4804 (tt) REVERT: D 199 MET cc_start: 0.6052 (ttp) cc_final: 0.5725 (ttp) REVERT: D 279 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7819 (pp) REVERT: D 290 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: D 301 MET cc_start: 0.8314 (pmm) cc_final: 0.7852 (pmm) REVERT: E 199 MET cc_start: -0.0672 (mmt) cc_final: -0.0915 (mmt) REVERT: F 267 LEU cc_start: 0.9230 (mt) cc_final: 0.9020 (pp) REVERT: G 45 ARG cc_start: 0.8828 (mmm160) cc_final: 0.8132 (mtm110) REVERT: G 207 MET cc_start: 0.8155 (ttm) cc_final: 0.7760 (mtp) REVERT: G 278 LEU cc_start: 0.8506 (tp) cc_final: 0.8177 (tt) REVERT: G 339 ASP cc_start: 0.9701 (t0) cc_final: 0.9252 (p0) REVERT: H 181 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8445 (p) REVERT: H 221 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7872 (mt-10) REVERT: H 278 LEU cc_start: 0.8766 (mt) cc_final: 0.8169 (mt) outliers start: 57 outliers final: 40 residues processed: 178 average time/residue: 0.2961 time to fit residues: 87.1801 Evaluate side-chains 170 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 65 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 177 optimal weight: 0.3980 chunk 228 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.097853 restraints weight = 64196.412| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.45 r_work: 0.3736 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21504 Z= 0.121 Angle : 0.625 12.932 29192 Z= 0.303 Chirality : 0.041 0.318 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.375 30.902 3088 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.16 % Allowed : 17.50 % Favored : 80.34 % 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: 0.71 (0.16), residues: 2752 helix: 1.11 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.46 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 351 HIS 0.009 0.001 HIS B 354 PHE 0.013 0.001 PHE F 281 TYR 0.059 0.001 TYR F 173 ARG 0.006 0.000 ARG F 172 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1260) hydrogen bonds : angle 4.10940 ( 3645) covalent geometry : bond 0.00276 (21504) covalent geometry : angle 0.62489 (29192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.8084 (tmm) cc_final: 0.7789 (tmm) REVERT: B 309 MET cc_start: 0.9002 (ppp) cc_final: 0.8747 (ppp) REVERT: C 288 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7262 (m-10) REVERT: D 61 ILE cc_start: 0.5439 (mm) cc_final: 0.4766 (tt) REVERT: D 279 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7814 (pp) REVERT: D 290 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6564 (m-10) REVERT: D 301 MET cc_start: 0.8351 (pmm) cc_final: 0.7889 (pmm) REVERT: E 83 MET cc_start: 0.5185 (mmp) cc_final: 0.4930 (mmm) REVERT: E 199 MET cc_start: -0.0751 (mmt) cc_final: -0.0998 (mmt) REVERT: F 267 LEU cc_start: 0.9246 (mt) cc_final: 0.9043 (pp) REVERT: G 45 ARG cc_start: 0.8770 (mmm160) cc_final: 0.8123 (mtm110) REVERT: G 207 MET cc_start: 0.8066 (ttm) cc_final: 0.7665 (mtp) REVERT: G 278 LEU cc_start: 0.8458 (tp) cc_final: 0.8122 (tt) REVERT: G 339 ASP cc_start: 0.9683 (t0) cc_final: 0.9205 (p0) REVERT: H 181 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8435 (p) REVERT: H 221 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7870 (mt-10) REVERT: H 278 LEU cc_start: 0.8741 (mt) cc_final: 0.8159 (mt) outliers start: 50 outliers final: 35 residues processed: 169 average time/residue: 0.3213 time to fit residues: 91.5792 Evaluate side-chains 165 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 78 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 232 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 GLN H 319 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.130938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.099191 restraints weight = 65941.400| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.90 r_work: 0.3704 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21504 Z= 0.125 Angle : 0.632 13.011 29192 Z= 0.304 Chirality : 0.041 0.350 3488 Planarity : 0.004 0.050 3840 Dihedral : 4.344 30.601 3088 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.07 % Allowed : 17.76 % Favored : 80.17 % 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: 0.74 (0.16), residues: 2752 helix: 1.14 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.45 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 351 HIS 0.008 0.001 HIS H 252 PHE 0.010 0.001 PHE D 192 TYR 0.060 0.001 TYR F 173 ARG 0.005 0.000 ARG F 172 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1260) hydrogen bonds : angle 4.07077 ( 3645) covalent geometry : bond 0.00287 (21504) covalent geometry : angle 0.63234 (29192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7575 (ppp) cc_final: 0.6825 (ppp) REVERT: B 207 MET cc_start: 0.8048 (tmm) cc_final: 0.7746 (ppp) REVERT: B 301 MET cc_start: 0.8419 (pmm) cc_final: 0.8215 (pmm) REVERT: B 309 MET cc_start: 0.8999 (ppp) cc_final: 0.8755 (ppp) REVERT: C 288 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7257 (m-10) REVERT: D 61 ILE cc_start: 0.5467 (mm) cc_final: 0.4770 (tt) REVERT: D 139 MET cc_start: 0.7802 (mpp) cc_final: 0.7539 (mpp) REVERT: D 279 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7804 (pp) REVERT: D 290 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: D 301 MET cc_start: 0.8333 (pmm) cc_final: 0.7876 (pmm) REVERT: E 83 MET cc_start: 0.5148 (mmp) cc_final: 0.4906 (mmm) REVERT: E 199 MET cc_start: -0.0781 (mmt) cc_final: -0.1034 (mmt) REVERT: G 45 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8189 (mtm110) REVERT: G 207 MET cc_start: 0.8109 (ttm) cc_final: 0.7717 (mtp) REVERT: G 278 LEU cc_start: 0.8436 (tp) cc_final: 0.8116 (tt) REVERT: G 322 LEU cc_start: 0.9512 (mt) cc_final: 0.9305 (pp) REVERT: G 339 ASP cc_start: 0.9687 (t0) cc_final: 0.9232 (p0) REVERT: H 181 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8447 (p) REVERT: H 221 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7950 (mt-10) REVERT: H 278 LEU cc_start: 0.8785 (mt) cc_final: 0.8215 (mt) outliers start: 48 outliers final: 39 residues processed: 170 average time/residue: 0.2869 time to fit residues: 80.6097 Evaluate side-chains 167 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 288 PHE Chi-restraints excluded: chain H residue 353 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 110 optimal weight: 0.8980 chunk 211 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.0370 chunk 164 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.131164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.099183 restraints weight = 66074.023| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.74 r_work: 0.3712 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21504 Z= 0.124 Angle : 0.649 15.040 29192 Z= 0.308 Chirality : 0.041 0.375 3488 Planarity : 0.004 0.050 3840 Dihedral : 4.310 30.613 3088 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.16 % Allowed : 17.84 % Favored : 80.00 % 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: 0.76 (0.16), residues: 2752 helix: 1.15 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.43 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 351 HIS 0.006 0.001 HIS H 252 PHE 0.011 0.001 PHE F 192 TYR 0.063 0.001 TYR F 173 ARG 0.004 0.000 ARG F 172 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1260) hydrogen bonds : angle 4.04136 ( 3645) covalent geometry : bond 0.00283 (21504) covalent geometry : angle 0.64867 (29192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7550 (ppp) cc_final: 0.6829 (ppp) REVERT: B 207 MET cc_start: 0.8086 (tmm) cc_final: 0.7803 (ppp) REVERT: B 301 MET cc_start: 0.8406 (pmm) cc_final: 0.8204 (pmm) REVERT: B 309 MET cc_start: 0.9003 (ppp) cc_final: 0.8754 (ppp) REVERT: C 288 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: C 339 ASP cc_start: 0.8662 (m-30) cc_final: 0.8018 (t0) REVERT: D 61 ILE cc_start: 0.5460 (mm) cc_final: 0.4767 (tt) REVERT: D 139 MET cc_start: 0.7831 (mpp) cc_final: 0.7577 (mpp) REVERT: D 279 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7785 (pp) REVERT: D 290 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6407 (m-10) REVERT: D 301 MET cc_start: 0.8289 (pmm) cc_final: 0.7764 (pmm) REVERT: E 199 MET cc_start: -0.0831 (mmt) cc_final: -0.1087 (mmt) REVERT: G 45 ARG cc_start: 0.8825 (mmm160) cc_final: 0.8199 (mtm110) REVERT: G 207 MET cc_start: 0.8086 (ttm) cc_final: 0.7685 (mtp) REVERT: G 278 LEU cc_start: 0.8425 (tp) cc_final: 0.8109 (tt) REVERT: G 309 MET cc_start: 0.8277 (ppp) cc_final: 0.7861 (ppp) REVERT: G 322 LEU cc_start: 0.9505 (mt) cc_final: 0.9299 (pp) REVERT: G 339 ASP cc_start: 0.9684 (t0) cc_final: 0.9215 (p0) REVERT: H 181 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8445 (p) outliers start: 50 outliers final: 42 residues processed: 170 average time/residue: 0.2934 time to fit residues: 82.8823 Evaluate side-chains 173 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 353 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 193 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 240 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 250 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 166 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.131676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.099065 restraints weight = 65385.914| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 3.85 r_work: 0.3716 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21504 Z= 0.123 Angle : 0.647 14.454 29192 Z= 0.307 Chirality : 0.041 0.321 3488 Planarity : 0.004 0.050 3840 Dihedral : 4.282 30.131 3088 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.20 % Allowed : 18.10 % Favored : 79.70 % 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: 0.81 (0.16), residues: 2752 helix: 1.18 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.40 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 351 HIS 0.006 0.001 HIS H 252 PHE 0.012 0.001 PHE F 192 TYR 0.055 0.001 TYR F 173 ARG 0.004 0.000 ARG F 172 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 1260) hydrogen bonds : angle 4.01449 ( 3645) covalent geometry : bond 0.00282 (21504) covalent geometry : angle 0.64709 (29192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14784.71 seconds wall clock time: 255 minutes 49.62 seconds (15349.62 seconds total)