Starting phenix.real_space_refine on Thu Mar 5 09:47:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y0d_33540/03_2026/7y0d_33540.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0d_33540/03_2026/7y0d_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 { model { file = "/net/cci-nas-00/data/ceres_data/7y0d_33540/03_2026/7y0d_33540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0d_33540/03_2026/7y0d_33540.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y0d_33540/03_2026/7y0d_33540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0d_33540/03_2026/7y0d_33540.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.07, per 1000 atoms: 0.24 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: 1.52 Conformation dependent library (CDL) restraints added in 1.1 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: 0.74 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: 3.41 Time building geometry restraints manager: 2.12 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: 0.01 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: 5.560 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.170 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- 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 : 13.56 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (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 ARG 0.012 0.000 ARG C 286 TYR 0.023 0.001 TYR B 173 PHE 0.026 0.001 PHE A 192 TRP 0.004 0.001 TRP C 351 HIS 0.003 0.001 HIS G 354 Details of bonding type rmsd covalent geometry : bond 0.00335 (21504) covalent geometry : angle 0.60582 (29192) hydrogen bonds : bond 0.16399 ( 1260) hydrogen bonds : angle 5.84283 ( 3645) *********************** 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 : 0.801 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: 0.1198 time to fit residues: 33.9913 Evaluate side-chains 121 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** C 127 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 HIS ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 HIS G 100 ASN G 319 HIS ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.134518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.100855 restraints weight = 62739.915| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 4.15 r_work: 0.3711 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0997 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= 0.145 Angle : 0.627 12.104 29192 Z= 0.314 Chirality : 0.041 0.231 3488 Planarity : 0.005 0.049 3840 Dihedral : 4.487 30.763 3088 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.65 % Allowed : 7.50 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2752 helix: 1.09 (0.13), residues: 1632 sheet: -0.82 (0.62), residues: 80 loop : -0.39 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.020 0.002 TYR E 54 PHE 0.016 0.001 PHE A 192 TRP 0.007 0.002 TRP H 351 HIS 0.010 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00327 (21504) covalent geometry : angle 0.62696 (29192) hydrogen bonds : bond 0.04435 ( 1260) hydrogen bonds : angle 4.57334 ( 3645) *********************** 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 157 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6912 (t80) cc_final: 0.6486 (t80) REVERT: B 54 TYR cc_start: 0.7036 (t80) cc_final: 0.6384 (t80) REVERT: B 309 MET cc_start: 0.8654 (ppp) cc_final: 0.8204 (ppp) REVERT: D 61 ILE cc_start: 0.5365 (mm) cc_final: 0.4432 (tt) REVERT: D 199 MET cc_start: 0.6492 (mtm) cc_final: 0.6155 (mtt) REVERT: E 350 MET cc_start: 0.9461 (tmm) cc_final: 0.9062 (tpt) REVERT: H 221 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7853 (mt-10) outliers start: 15 outliers final: 9 residues processed: 150 average time/residue: 0.1138 time to fit residues: 29.2497 Evaluate side-chains 138 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 234 ASP 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 F residue 199 MET Chi-restraints excluded: chain G residue 205 LEU 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 47 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 165 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 255 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 269 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.134330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.100118 restraints weight = 63435.074| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.88 r_work: 0.3733 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1308 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= 0.122 Angle : 0.590 11.285 29192 Z= 0.291 Chirality : 0.040 0.258 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.350 29.746 3088 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.21 % Allowed : 10.91 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 2752 helix: 1.15 (0.13), residues: 1640 sheet: None (None), residues: 0 loop : -0.36 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.023 0.001 TYR F 173 PHE 0.013 0.001 PHE A 192 TRP 0.007 0.001 TRP C 351 HIS 0.007 0.001 HIS H 252 Details of bonding type rmsd covalent geometry : bond 0.00273 (21504) covalent geometry : angle 0.58993 (29192) hydrogen bonds : bond 0.03813 ( 1260) hydrogen bonds : angle 4.27180 ( 3645) *********************** 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: 28 poor density : 143 time to evaluate : 0.808 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: 0.7110 (t80) cc_final: 0.6780 (t80) REVERT: A 309 MET cc_start: 0.7971 (ppp) cc_final: 0.7333 (ppp) REVERT: B 165 GLN cc_start: 0.9242 (mp10) cc_final: 0.9017 (mp10) REVERT: B 309 MET cc_start: 0.8612 (ppp) cc_final: 0.8324 (ppp) REVERT: C 350 MET cc_start: 0.8549 (tmm) cc_final: 0.8312 (tpt) REVERT: D 61 ILE cc_start: 0.5282 (mm) cc_final: 0.4334 (tt) REVERT: D 199 MET cc_start: 0.6373 (mtm) cc_final: 0.5968 (mtt) REVERT: D 290 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: D 301 MET cc_start: 0.8175 (pmm) cc_final: 0.7971 (pmm) REVERT: E 199 MET cc_start: -0.0858 (OUTLIER) cc_final: -0.1093 (mmt) REVERT: F 139 MET cc_start: 0.7745 (mmm) cc_final: 0.7356 (mmm) REVERT: G 45 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8204 (mtm110) REVERT: G 199 MET cc_start: 0.6513 (ttp) cc_final: 0.6292 (ttp) REVERT: G 207 MET cc_start: 0.8028 (ttm) cc_final: 0.7646 (mtp) REVERT: H 221 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7803 (mt-10) outliers start: 28 outliers final: 19 residues processed: 160 average time/residue: 0.1346 time to fit residues: 34.8795 Evaluate side-chains 151 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 230 LYS Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 142 VAL 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 199 MET Chi-restraints excluded: chain E residue 268 GLU 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 104 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 116 THR 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 15 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 142 optimal weight: 0.0870 chunk 211 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 GLN H 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.134104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.098774 restraints weight = 64033.545| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.65 r_work: 0.3750 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21504 Z= 0.119 Angle : 0.579 14.761 29192 Z= 0.285 Chirality : 0.039 0.150 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.286 30.238 3088 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.47 % Allowed : 12.89 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2752 helix: 1.18 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.31 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.015 0.001 TYR B 173 PHE 0.015 0.001 PHE F 281 TRP 0.007 0.001 TRP C 351 HIS 0.005 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00265 (21504) covalent geometry : angle 0.57935 (29192) hydrogen bonds : bond 0.03606 ( 1260) hydrogen bonds : angle 4.13825 ( 3645) *********************** 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 179 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7079 (t80) cc_final: 0.6715 (t80) REVERT: C 288 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: D 61 ILE cc_start: 0.5353 (mm) cc_final: 0.4451 (tt) REVERT: D 199 MET cc_start: 0.6259 (mtm) cc_final: 0.5702 (mtt) REVERT: D 290 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6446 (m-10) REVERT: D 350 MET cc_start: 0.8963 (ppp) cc_final: 0.8738 (ppp) REVERT: E 54 TYR cc_start: 0.7658 (t80) cc_final: 0.7378 (t80) REVERT: E 199 MET cc_start: -0.0829 (OUTLIER) cc_final: -0.1083 (mmt) REVERT: G 45 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8214 (mtm180) REVERT: G 207 MET cc_start: 0.8095 (ttm) cc_final: 0.7568 (mtp) REVERT: G 322 LEU cc_start: 0.9477 (mt) cc_final: 0.9273 (pp) outliers start: 34 outliers final: 19 residues processed: 169 average time/residue: 0.1273 time to fit residues: 35.8034 Evaluate side-chains 151 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 234 ASP 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 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 199 MET Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 268 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 31 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 331 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.133959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.097462 restraints weight = 60567.827| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 4.09 r_work: 0.3642 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 21504 Z= 0.274 Angle : 0.723 14.933 29192 Z= 0.359 Chirality : 0.044 0.194 3488 Planarity : 0.005 0.051 3840 Dihedral : 4.837 30.388 3088 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.16 % Allowed : 14.35 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2752 helix: 0.87 (0.13), residues: 1680 sheet: -1.63 (0.58), residues: 80 loop : -0.58 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 150 TYR 0.021 0.002 TYR F 173 PHE 0.019 0.002 PHE F 281 TRP 0.009 0.001 TRP E 351 HIS 0.007 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00626 (21504) covalent geometry : angle 0.72291 (29192) hydrogen bonds : bond 0.04448 ( 1260) hydrogen bonds : angle 4.44419 ( 3645) *********************** 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 179 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 129 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7126 (t80) cc_final: 0.6844 (t80) REVERT: B 301 MET cc_start: 0.8456 (pmm) cc_final: 0.7826 (pmm) REVERT: B 309 MET cc_start: 0.8754 (ppp) cc_final: 0.8431 (ppp) REVERT: C 288 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: D 61 ILE cc_start: 0.5794 (mm) cc_final: 0.4657 (tt) REVERT: D 199 MET cc_start: 0.6331 (mtm) cc_final: 0.6022 (mtt) REVERT: D 279 LEU cc_start: 0.8177 (mm) cc_final: 0.7846 (pp) REVERT: D 290 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6658 (m-10) REVERT: D 309 MET cc_start: 0.8684 (tmm) cc_final: 0.8481 (tmm) REVERT: E 199 MET cc_start: -0.0828 (OUTLIER) cc_final: -0.1127 (mmt) REVERT: F 281 PHE cc_start: 0.7852 (t80) cc_final: 0.7508 (t80) REVERT: G 207 MET cc_start: 0.8221 (ttm) cc_final: 0.7844 (mtp) outliers start: 50 outliers final: 30 residues processed: 168 average time/residue: 0.1139 time to fit residues: 32.7166 Evaluate side-chains 153 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 233 LEU 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 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 222 LEU 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 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain G residue 77 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 116 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 191 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 208 optimal weight: 0.8980 chunk 259 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** 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 = 0.4491 r_free = 0.4491 target = 0.134371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.098401 restraints weight = 61790.513| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.77 r_work: 0.3700 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1806 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= 0.150 Angle : 0.635 14.432 29192 Z= 0.309 Chirality : 0.041 0.183 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.557 31.262 3088 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.94 % Allowed : 15.82 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2752 helix: 1.03 (0.13), residues: 1680 sheet: -1.49 (0.60), residues: 80 loop : -0.54 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.031 0.001 TYR F 173 PHE 0.010 0.001 PHE G 288 TRP 0.008 0.001 TRP B 351 HIS 0.012 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00346 (21504) covalent geometry : angle 0.63519 (29192) hydrogen bonds : bond 0.03886 ( 1260) hydrogen bonds : angle 4.20677 ( 3645) *********************** 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 181 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.8145 (tmm) cc_final: 0.7862 (ppp) REVERT: B 301 MET cc_start: 0.8457 (pmm) cc_final: 0.7906 (pmm) REVERT: B 309 MET cc_start: 0.8810 (ppp) cc_final: 0.8527 (ppp) REVERT: C 288 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7276 (m-10) REVERT: D 61 ILE cc_start: 0.5396 (mm) cc_final: 0.4624 (tt) REVERT: D 279 LEU cc_start: 0.8178 (mm) cc_final: 0.7837 (pp) REVERT: D 290 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: E 199 MET cc_start: -0.0919 (OUTLIER) cc_final: -0.1210 (mmt) REVERT: F 281 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7401 (t80) REVERT: G 45 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8146 (mtm110) REVERT: G 207 MET cc_start: 0.8166 (ttm) cc_final: 0.7808 (mtp) outliers start: 45 outliers final: 26 residues processed: 171 average time/residue: 0.1302 time to fit residues: 36.8805 Evaluate side-chains 156 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain B residue 230 LYS 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 166 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 229 LEU 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 199 MET Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 281 PHE 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 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 116 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 213 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 103 optimal weight: 0.0870 chunk 218 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 248 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** 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** D 100 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.139904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.102209 restraints weight = 56507.001| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 4.39 r_work: 0.3698 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21504 Z= 0.145 Angle : 0.636 14.620 29192 Z= 0.309 Chirality : 0.041 0.238 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.501 33.903 3088 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.07 % Allowed : 16.16 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.16), residues: 2752 helix: 1.08 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.47 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 353 TYR 0.041 0.001 TYR F 173 PHE 0.012 0.001 PHE F 281 TRP 0.008 0.001 TRP C 351 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00331 (21504) covalent geometry : angle 0.63598 (29192) hydrogen bonds : bond 0.03790 ( 1260) hydrogen bonds : angle 4.16370 ( 3645) *********************** 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 176 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6631 (t80) cc_final: 0.6391 (t80) REVERT: A 309 MET cc_start: 0.7614 (ppp) cc_final: 0.7008 (ppp) REVERT: B 207 MET cc_start: 0.8208 (tmm) cc_final: 0.7872 (ppp) REVERT: B 301 MET cc_start: 0.8368 (pmm) cc_final: 0.7893 (pmm) REVERT: B 309 MET cc_start: 0.8925 (ppp) cc_final: 0.8668 (ppp) REVERT: C 288 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: D 61 ILE cc_start: 0.5362 (mm) cc_final: 0.4589 (tt) REVERT: D 279 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7853 (pp) REVERT: D 290 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6636 (m-10) REVERT: E 199 MET cc_start: -0.0916 (OUTLIER) cc_final: -0.1214 (mmt) REVERT: F 281 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7512 (t80) REVERT: G 45 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8120 (mtm110) REVERT: G 207 MET cc_start: 0.8179 (ttm) cc_final: 0.7777 (mtp) REVERT: G 278 LEU cc_start: 0.8485 (tp) cc_final: 0.8158 (tt) REVERT: G 339 ASP cc_start: 0.9700 (t0) cc_final: 0.9253 (p0) outliers start: 48 outliers final: 32 residues processed: 164 average time/residue: 0.1251 time to fit residues: 34.8347 Evaluate side-chains 162 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 128 THR Chi-restraints excluded: chain B residue 233 LEU 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 177 LEU Chi-restraints excluded: chain D residue 229 LEU 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 199 MET Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 281 PHE 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 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 116 THR 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 Chi-restraints excluded: chain H residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 122 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 HIS H 319 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.137547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.101708 restraints weight = 58204.857| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 4.30 r_work: 0.3681 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21504 Z= 0.159 Angle : 0.644 12.864 29192 Z= 0.313 Chirality : 0.041 0.211 3488 Planarity : 0.004 0.051 3840 Dihedral : 4.520 32.669 3088 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.07 % Allowed : 16.90 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2752 helix: 1.08 (0.13), residues: 1680 sheet: -1.44 (0.60), residues: 80 loop : -0.52 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 172 TYR 0.041 0.002 TYR F 173 PHE 0.010 0.001 PHE F 281 TRP 0.009 0.001 TRP C 351 HIS 0.013 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00365 (21504) covalent geometry : angle 0.64384 (29192) hydrogen bonds : bond 0.03803 ( 1260) hydrogen bonds : angle 4.16622 ( 3645) *********************** 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 176 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6592 (t80) cc_final: 0.6359 (t80) REVERT: B 207 MET cc_start: 0.8206 (tmm) cc_final: 0.7865 (ppp) REVERT: B 301 MET cc_start: 0.8338 (pmm) cc_final: 0.7881 (pmm) REVERT: B 309 MET cc_start: 0.8961 (ppp) cc_final: 0.8716 (ppp) REVERT: C 207 MET cc_start: 0.7824 (ptp) cc_final: 0.7374 (pmm) REVERT: C 288 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: D 61 ILE cc_start: 0.5407 (mm) cc_final: 0.4621 (tt) REVERT: D 279 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7843 (pp) REVERT: D 290 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6637 (m-10) REVERT: D 301 MET cc_start: 0.8385 (pmm) cc_final: 0.7863 (pmm) REVERT: E 199 MET cc_start: -0.0925 (OUTLIER) cc_final: -0.1219 (mmt) REVERT: F 281 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7574 (t80) REVERT: G 45 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8160 (mtm110) REVERT: G 207 MET cc_start: 0.8207 (ttm) cc_final: 0.7824 (mtp) REVERT: G 278 LEU cc_start: 0.8496 (tp) cc_final: 0.8032 (tt) outliers start: 48 outliers final: 35 residues processed: 163 average time/residue: 0.1210 time to fit residues: 33.5008 Evaluate side-chains 165 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 230 LYS Chi-restraints excluded: chain B residue 233 LEU 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 62 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 229 LEU 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 199 MET Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 281 PHE 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 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 THR 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 Chi-restraints excluded: chain H residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 260 optimal weight: 10.0000 chunk 214 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 262 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** 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** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.132553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.098914 restraints weight = 63975.340| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.93 r_work: 0.3708 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21504 Z= 0.138 Angle : 0.628 13.164 29192 Z= 0.305 Chirality : 0.041 0.185 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.435 31.960 3088 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.94 % Allowed : 17.11 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2752 helix: 1.14 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.47 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 353 TYR 0.048 0.001 TYR F 173 PHE 0.011 0.001 PHE G 288 TRP 0.012 0.001 TRP G 351 HIS 0.009 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00318 (21504) covalent geometry : angle 0.62799 (29192) hydrogen bonds : bond 0.03653 ( 1260) hydrogen bonds : angle 4.10067 ( 3645) *********************** 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 175 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7627 (ppp) cc_final: 0.6708 (ppp) REVERT: B 207 MET cc_start: 0.8195 (tmm) cc_final: 0.7837 (ppp) REVERT: B 301 MET cc_start: 0.8292 (pmm) cc_final: 0.7824 (pmm) REVERT: B 309 MET cc_start: 0.9011 (ppp) cc_final: 0.8778 (ppp) REVERT: C 288 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7332 (m-10) REVERT: C 339 ASP cc_start: 0.8698 (m-30) cc_final: 0.8080 (t0) REVERT: D 61 ILE cc_start: 0.5533 (mm) cc_final: 0.4795 (tt) REVERT: D 279 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7755 (pp) REVERT: D 290 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6495 (m-10) REVERT: D 301 MET cc_start: 0.8273 (pmm) cc_final: 0.7778 (pmm) REVERT: E 83 MET cc_start: 0.5057 (mmp) cc_final: 0.4783 (mmm) REVERT: E 199 MET cc_start: -0.1044 (OUTLIER) cc_final: -0.1329 (mmt) REVERT: F 281 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7661 (t80) REVERT: G 45 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8130 (mtm110) REVERT: G 207 MET cc_start: 0.8165 (ttm) cc_final: 0.7785 (mtp) REVERT: G 278 LEU cc_start: 0.8415 (tp) cc_final: 0.8071 (tt) REVERT: G 339 ASP cc_start: 0.9700 (t0) cc_final: 0.9267 (p0) outliers start: 45 outliers final: 35 residues processed: 164 average time/residue: 0.1260 time to fit residues: 34.7513 Evaluate side-chains 167 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 128 THR Chi-restraints excluded: chain C residue 32 THR 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 62 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 229 LEU 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 199 MET Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 281 PHE 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 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 THR 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 Chi-restraints excluded: chain H residue 283 VAL 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 76 optimal weight: 0.7980 chunk 41 optimal weight: 0.0770 chunk 244 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 240 optimal weight: 0.8980 chunk 125 optimal weight: 0.0010 chunk 36 optimal weight: 1.9990 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** 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** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 HIS H 319 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.132337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.099279 restraints weight = 65589.521| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.89 r_work: 0.3728 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2125 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= 0.118 Angle : 0.631 13.449 29192 Z= 0.303 Chirality : 0.040 0.177 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.327 31.655 3088 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.72 % Allowed : 17.46 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2752 helix: 1.19 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.39 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 227 TYR 0.053 0.001 TYR F 173 PHE 0.011 0.001 PHE F 281 TRP 0.011 0.001 TRP C 351 HIS 0.013 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00266 (21504) covalent geometry : angle 0.63072 (29192) hydrogen bonds : bond 0.03540 ( 1260) hydrogen bonds : angle 4.04257 ( 3645) ********************** 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 168 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7595 (ppp) cc_final: 0.6668 (ppp) REVERT: B 207 MET cc_start: 0.8223 (tmm) cc_final: 0.7828 (ppp) REVERT: B 301 MET cc_start: 0.8363 (pmm) cc_final: 0.7810 (pmm) REVERT: B 309 MET cc_start: 0.9001 (ppp) cc_final: 0.8769 (ppp) REVERT: C 288 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: C 339 ASP cc_start: 0.8650 (m-30) cc_final: 0.8012 (t0) REVERT: D 61 ILE cc_start: 0.5412 (mm) cc_final: 0.4735 (tt) REVERT: D 279 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7723 (pp) REVERT: D 290 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: D 301 MET cc_start: 0.8316 (pmm) cc_final: 0.7783 (pmm) REVERT: E 199 MET cc_start: -0.1116 (OUTLIER) cc_final: -0.1400 (mmt) REVERT: F 281 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7595 (t80) REVERT: G 45 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8127 (mtm110) REVERT: G 207 MET cc_start: 0.8142 (ttm) cc_final: 0.7763 (mtp) REVERT: G 278 LEU cc_start: 0.8402 (tp) cc_final: 0.8060 (tt) REVERT: G 339 ASP cc_start: 0.9690 (t0) cc_final: 0.9245 (p0) outliers start: 40 outliers final: 27 residues processed: 157 average time/residue: 0.1291 time to fit residues: 33.8586 Evaluate side-chains 157 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 A residue 319 HIS Chi-restraints excluded: chain B residue 87 VAL 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 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 177 LEU 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 199 MET Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 281 PHE 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 202 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 178 ASP 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 191 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 264 optimal weight: 0.4980 chunk 253 optimal weight: 0.7980 chunk 215 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 213 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.132562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.098765 restraints weight = 64309.416| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.77 r_work: 0.3724 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21504 Z= 0.129 Angle : 0.638 13.249 29192 Z= 0.306 Chirality : 0.040 0.240 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.338 31.546 3088 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.68 % Allowed : 17.67 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2752 helix: 1.22 (0.13), residues: 1672 sheet: None (None), residues: 0 loop : -0.35 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 353 TYR 0.054 0.001 TYR F 173 PHE 0.013 0.001 PHE F 281 TRP 0.012 0.001 TRP C 351 HIS 0.011 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00298 (21504) covalent geometry : angle 0.63815 (29192) hydrogen bonds : bond 0.03563 ( 1260) hydrogen bonds : angle 4.04999 ( 3645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6819.28 seconds wall clock time: 116 minutes 45.03 seconds (7005.03 seconds total)