Starting phenix.real_space_refine on Sun Feb 18 07:40:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0d_33540/02_2024/7y0d_33540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0d_33540/02_2024/7y0d_33540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0d_33540/02_2024/7y0d_33540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0d_33540/02_2024/7y0d_33540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0d_33540/02_2024/7y0d_33540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y0d_33540/02_2024/7y0d_33540.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 13136 2.51 5 N 3824 2.21 5 O 4200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "H GLU 206": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21224 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "B" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "C" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "E" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "F" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "G" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain: "H" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2653 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Time building chain proxies: 11.26, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.76 Conformation dependent library (CDL) restraints added in 3.9 seconds 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 20 sheets defined 66.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 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: 6.82 Time building geometry restraints manager: 9.44 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: 97.28 - 104.62: 309 104.62 - 111.96: 10957 111.96 - 119.30: 7309 119.30 - 126.63: 10447 126.63 - 133.97: 170 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 2.440 nonbonded pdb=" OG SER D 156 " pdb=" OD2 ASP D 225 " model vdw 2.177 2.440 nonbonded pdb=" OE2 GLU E 188 " pdb=" OH TYR E 251 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR B 111 " pdb=" OE1 GLU B 122 " model vdw 2.208 2.440 nonbonded pdb=" OD1 ASP G 250 " pdb=" OG SER G 303 " model vdw 2.218 2.440 ... (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 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.910 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 56.310 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.720 ------------------------------------------------------------------------------- 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= 0.224 Angle : 0.606 9.611 29192 Z= 0.310 Chirality : 0.041 0.159 3488 Planarity : 0.004 0.060 3840 Dihedral : 13.787 89.057 8080 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2752 helix: 1.16 (0.13), residues: 1568 sheet: -0.58 (0.64), residues: 80 loop : -0.24 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 351 HIS 0.003 0.001 HIS G 354 PHE 0.026 0.001 PHE A 192 TYR 0.023 0.001 TYR B 173 ARG 0.012 0.000 ARG C 286 *********************** 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 fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.547 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: 0.2777 time to fit residues: 77.5493 Evaluate side-chains 120 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 0.0980 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 247 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 HIS 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21504 Z= 0.209 Angle : 0.603 11.908 29192 Z= 0.301 Chirality : 0.040 0.151 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.429 30.748 3088 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.65 % Allowed : 7.59 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2752 helix: 1.21 (0.13), residues: 1624 sheet: -0.77 (0.62), residues: 80 loop : -0.32 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 351 HIS 0.006 0.001 HIS A 319 PHE 0.017 0.001 PHE A 192 TYR 0.020 0.002 TYR E 54 ARG 0.006 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6412 (t80) cc_final: 0.5872 (t80) REVERT: B 199 MET cc_start: 0.7977 (ttm) cc_final: 0.7641 (ttm) REVERT: B 309 MET cc_start: 0.8490 (ppp) cc_final: 0.8060 (ppp) REVERT: D 61 ILE cc_start: 0.5168 (mm) cc_final: 0.4513 (tt) REVERT: D 199 MET cc_start: 0.6340 (mtm) cc_final: 0.6029 (mtt) REVERT: D 290 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: H 221 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7288 (mt-10) outliers start: 15 outliers final: 9 residues processed: 153 average time/residue: 0.2984 time to fit residues: 75.5507 Evaluate side-chains 144 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 2.470 ------------------------------------------------------------------------------- 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 D residue 290 TYR 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 137 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 0.3980 chunk 267 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS B 127 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 GLN ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21504 Z= 0.248 Angle : 0.603 11.232 29192 Z= 0.300 Chirality : 0.040 0.210 3488 Planarity : 0.004 0.048 3840 Dihedral : 4.471 30.036 3088 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.29 % Allowed : 10.39 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2752 helix: 1.19 (0.13), residues: 1632 sheet: -1.05 (0.61), residues: 80 loop : -0.42 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 351 HIS 0.005 0.001 HIS A 319 PHE 0.013 0.001 PHE A 192 TYR 0.022 0.002 TYR H 173 ARG 0.004 0.000 ARG B 35 *********************** 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 169 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6608 (t80) cc_final: 0.6156 (t80) REVERT: A 309 MET cc_start: 0.7497 (ppp) cc_final: 0.7011 (ppp) REVERT: B 309 MET cc_start: 0.8502 (ppp) cc_final: 0.8232 (ppp) REVERT: C 288 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: C 350 MET cc_start: 0.8276 (tmm) cc_final: 0.7876 (tpt) REVERT: D 61 ILE cc_start: 0.5330 (mm) cc_final: 0.4541 (tt) REVERT: D 290 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6308 (m-10) REVERT: D 301 MET cc_start: 0.8107 (pmm) cc_final: 0.7720 (pmm) REVERT: E 199 MET cc_start: -0.0341 (mmt) cc_final: -0.0548 (mmt) REVERT: E 267 LEU cc_start: 0.9401 (mt) cc_final: 0.9173 (pp) REVERT: G 199 MET cc_start: 0.6499 (ttp) cc_final: 0.6202 (ttp) REVERT: H 173 TYR cc_start: 0.7458 (m-10) cc_final: 0.7181 (m-80) REVERT: H 207 MET cc_start: 0.8110 (ttm) cc_final: 0.7545 (ttm) REVERT: H 221 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7290 (mt-10) outliers start: 30 outliers final: 20 residues processed: 158 average time/residue: 0.2876 time to fit residues: 76.9353 Evaluate side-chains 151 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 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 290 TYR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain F residue 278 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 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 244 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 0.6980 chunk 262 optimal weight: 0.0670 chunk 129 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21504 Z= 0.186 Angle : 0.569 10.949 29192 Z= 0.281 Chirality : 0.039 0.150 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.338 30.694 3088 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.34 % Allowed : 12.67 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2752 helix: 1.30 (0.13), residues: 1632 sheet: -0.98 (0.62), residues: 80 loop : -0.40 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 351 HIS 0.005 0.001 HIS A 319 PHE 0.012 0.001 PHE F 281 TYR 0.018 0.001 TYR E 54 ARG 0.003 0.000 ARG B 35 *********************** 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 174 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6514 (t80) cc_final: 0.6147 (t80) REVERT: C 288 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6731 (m-10) REVERT: D 61 ILE cc_start: 0.5257 (mm) cc_final: 0.4635 (tt) REVERT: D 290 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6339 (m-10) REVERT: D 301 MET cc_start: 0.8018 (pmm) cc_final: 0.7599 (pmm) REVERT: D 350 MET cc_start: 0.8835 (ppp) cc_final: 0.8578 (ppp) REVERT: E 267 LEU cc_start: 0.9436 (mt) cc_final: 0.9158 (pp) REVERT: G 207 MET cc_start: 0.7843 (ttm) cc_final: 0.6971 (mtp) REVERT: H 207 MET cc_start: 0.8020 (ttm) cc_final: 0.7340 (ttm) outliers start: 31 outliers final: 18 residues processed: 165 average time/residue: 0.2796 time to fit residues: 76.2675 Evaluate side-chains 150 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 C residue 32 THR 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 290 TYR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 301 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 177 LEU Chi-restraints excluded: chain G residue 202 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1448 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= 0.223 Angle : 0.591 11.474 29192 Z= 0.293 Chirality : 0.040 0.164 3488 Planarity : 0.004 0.047 3840 Dihedral : 4.399 30.167 3088 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.03 % Allowed : 13.10 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2752 helix: 1.26 (0.13), residues: 1632 sheet: -1.11 (0.62), residues: 80 loop : -0.43 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 351 HIS 0.006 0.001 HIS A 319 PHE 0.010 0.001 PHE A 192 TYR 0.034 0.001 TYR H 173 ARG 0.003 0.000 ARG G 356 *********************** 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 191 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 144 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7281 (ppp) cc_final: 0.6694 (ppp) REVERT: B 165 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8864 (mp10) REVERT: B 309 MET cc_start: 0.8652 (ppp) cc_final: 0.8335 (ppp) REVERT: C 288 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: C 339 ASP cc_start: 0.8307 (m-30) cc_final: 0.7534 (t0) REVERT: D 61 ILE cc_start: 0.5514 (mm) cc_final: 0.4877 (tt) REVERT: D 290 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.6334 (m-10) REVERT: D 301 MET cc_start: 0.7977 (pmm) cc_final: 0.7530 (pmm) REVERT: E 199 MET cc_start: -0.0471 (mmt) cc_final: -0.0752 (mmt) REVERT: E 350 MET cc_start: 0.9300 (tmm) cc_final: 0.8966 (ppp) REVERT: H 207 MET cc_start: 0.8170 (ttm) cc_final: 0.7804 (ttm) outliers start: 47 outliers final: 29 residues processed: 181 average time/residue: 0.2881 time to fit residues: 85.5550 Evaluate side-chains 164 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 165 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 354 HIS 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 166 THR Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 301 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 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 88 optimal weight: 0.0070 chunk 236 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1618 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= 0.178 Angle : 0.594 14.743 29192 Z= 0.288 Chirality : 0.040 0.285 3488 Planarity : 0.004 0.048 3840 Dihedral : 4.297 33.390 3088 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.94 % Allowed : 14.74 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 2752 helix: 1.29 (0.13), residues: 1640 sheet: None (None), residues: 0 loop : -0.37 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 351 HIS 0.006 0.001 HIS A 319 PHE 0.012 0.001 PHE F 288 TYR 0.037 0.001 TYR F 173 ARG 0.004 0.000 ARG F 172 *********************** 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 190 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6143 (t80) cc_final: 0.5664 (t80) REVERT: A 309 MET cc_start: 0.7338 (ppp) cc_final: 0.6814 (ppp) REVERT: B 165 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8870 (mp10) REVERT: B 309 MET cc_start: 0.8790 (ppp) cc_final: 0.8565 (ppp) REVERT: C 288 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6907 (m-10) REVERT: C 339 ASP cc_start: 0.8266 (m-30) cc_final: 0.7512 (t0) REVERT: D 61 ILE cc_start: 0.5226 (mm) cc_final: 0.4723 (tt) REVERT: D 290 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6399 (m-10) REVERT: E 267 LEU cc_start: 0.9381 (mt) cc_final: 0.9174 (pp) REVERT: F 267 LEU cc_start: 0.8975 (mt) cc_final: 0.8772 (pp) REVERT: G 207 MET cc_start: 0.7835 (ttm) cc_final: 0.7064 (mtp) REVERT: H 173 TYR cc_start: 0.7628 (m-80) cc_final: 0.7419 (m-80) outliers start: 45 outliers final: 31 residues processed: 179 average time/residue: 0.2963 time to fit residues: 87.1661 Evaluate side-chains 166 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain 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 165 GLN Chi-restraints excluded: chain B residue 354 HIS 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 290 TYR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 301 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 G residue 353 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 192 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 262 optimal weight: 0.0980 chunk 164 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21504 Z= 0.173 Angle : 0.601 12.190 29192 Z= 0.291 Chirality : 0.040 0.282 3488 Planarity : 0.004 0.048 3840 Dihedral : 4.248 31.768 3088 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.98 % Allowed : 15.56 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2752 helix: 1.33 (0.13), residues: 1640 sheet: None (None), residues: 0 loop : -0.34 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 351 HIS 0.013 0.001 HIS A 319 PHE 0.012 0.001 PHE F 288 TYR 0.048 0.001 TYR F 173 ARG 0.004 0.000 ARG G 71 *********************** 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 180 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 134 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6314 (t80) cc_final: 0.5961 (t80) REVERT: C 288 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6909 (m-10) REVERT: C 339 ASP cc_start: 0.8288 (m-30) cc_final: 0.7537 (t0) REVERT: D 61 ILE cc_start: 0.5168 (mm) cc_final: 0.4676 (tt) REVERT: D 199 MET cc_start: 0.6110 (ttp) cc_final: 0.5901 (ttp) REVERT: D 290 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6298 (m-10) REVERT: E 199 MET cc_start: -0.0520 (mmt) cc_final: -0.0790 (mmt) REVERT: E 267 LEU cc_start: 0.9390 (mt) cc_final: 0.9172 (pp) REVERT: G 207 MET cc_start: 0.8018 (ttm) cc_final: 0.7214 (mtp) outliers start: 46 outliers final: 35 residues processed: 168 average time/residue: 0.2958 time to fit residues: 80.9612 Evaluate side-chains 166 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 233 LEU 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 290 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 301 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 G residue 353 ARG 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 268 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 288 PHE Chi-restraints excluded: chain H residue 353 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.0050 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1822 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= 0.218 Angle : 0.617 15.799 29192 Z= 0.301 Chirality : 0.040 0.267 3488 Planarity : 0.004 0.049 3840 Dihedral : 4.362 31.530 3088 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.11 % Allowed : 16.16 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2752 helix: 1.21 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.37 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 351 HIS 0.006 0.001 HIS A 319 PHE 0.023 0.001 PHE F 288 TYR 0.011 0.001 TYR F 173 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 131 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7994 (mmm) cc_final: 0.7619 (mmm) REVERT: A 173 TYR cc_start: 0.6077 (t80) cc_final: 0.5859 (t80) REVERT: A 309 MET cc_start: 0.7115 (ppp) cc_final: 0.6442 (ppp) REVERT: C 288 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6816 (m-10) REVERT: C 339 ASP cc_start: 0.8284 (m-30) cc_final: 0.7536 (t0) REVERT: D 61 ILE cc_start: 0.5314 (mm) cc_final: 0.4762 (tt) REVERT: D 290 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6358 (m-10) REVERT: D 350 MET cc_start: 0.8548 (ppp) cc_final: 0.8289 (ppp) REVERT: E 83 MET cc_start: 0.4650 (mmp) cc_final: 0.4438 (mmm) REVERT: E 199 MET cc_start: -0.0585 (mmt) cc_final: -0.0868 (mmt) REVERT: E 267 LEU cc_start: 0.9392 (mt) cc_final: 0.9168 (pp) REVERT: E 350 MET cc_start: 0.9316 (tmm) cc_final: 0.8926 (ppp) REVERT: G 207 MET cc_start: 0.7954 (ttm) cc_final: 0.7149 (mtp) outliers start: 49 outliers final: 39 residues processed: 165 average time/residue: 0.2900 time to fit residues: 79.2070 Evaluate side-chains 171 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain 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 233 LEU 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 160 LEU 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 278 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 268 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 301 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 G residue 353 ARG 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 268 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 288 PHE Chi-restraints excluded: chain H residue 353 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 229 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 231 optimal weight: 0.4980 chunk 243 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1891 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= 0.179 Angle : 0.616 14.265 29192 Z= 0.296 Chirality : 0.040 0.257 3488 Planarity : 0.004 0.048 3840 Dihedral : 4.283 30.936 3088 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.98 % Allowed : 16.29 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2752 helix: 1.23 (0.13), residues: 1688 sheet: None (None), residues: 0 loop : -0.38 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 351 HIS 0.015 0.001 HIS A 319 PHE 0.029 0.001 PHE F 288 TYR 0.024 0.001 TYR H 173 ARG 0.004 0.000 ARG F 172 *********************** 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 179 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 133 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.6046 (t80) cc_final: 0.5837 (t80) REVERT: A 309 MET cc_start: 0.7145 (ppp) cc_final: 0.6548 (ppp) REVERT: B 165 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8787 (mp10) REVERT: C 288 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: C 339 ASP cc_start: 0.8256 (m-30) cc_final: 0.7517 (t0) REVERT: D 61 ILE cc_start: 0.5181 (mm) cc_final: 0.4695 (tt) REVERT: D 290 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: D 350 MET cc_start: 0.8572 (ppp) cc_final: 0.8348 (ppp) REVERT: E 199 MET cc_start: -0.0560 (mmt) cc_final: -0.0844 (mmt) REVERT: E 267 LEU cc_start: 0.9393 (mt) cc_final: 0.9163 (pp) REVERT: E 350 MET cc_start: 0.9352 (tmm) cc_final: 0.8943 (ppp) REVERT: G 207 MET cc_start: 0.7947 (ttm) cc_final: 0.7373 (mtp) REVERT: H 278 LEU cc_start: 0.8913 (tp) cc_final: 0.8656 (tt) outliers start: 46 outliers final: 36 residues processed: 164 average time/residue: 0.2781 time to fit residues: 75.3338 Evaluate side-chains 168 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 233 LEU 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 160 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 278 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 268 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 301 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 G residue 353 ARG 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 268 GLU 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 160 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 215 optimal weight: 0.0770 chunk 22 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 HIS ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1956 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= 0.195 Angle : 0.622 13.860 29192 Z= 0.300 Chirality : 0.040 0.255 3488 Planarity : 0.004 0.050 3840 Dihedral : 4.302 30.826 3088 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.03 % Allowed : 16.47 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.16), residues: 2752 helix: 1.25 (0.13), residues: 1688 sheet: None (None), residues: 0 loop : -0.39 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 351 HIS 0.012 0.001 HIS B 354 PHE 0.029 0.001 PHE F 288 TYR 0.028 0.001 TYR H 173 ARG 0.003 0.000 ARG A 227 ********************** 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 177 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7163 (ppp) cc_final: 0.6580 (ppp) REVERT: B 165 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8803 (mp10) REVERT: C 288 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6836 (m-10) REVERT: C 339 ASP cc_start: 0.8235 (m-30) cc_final: 0.7500 (t0) REVERT: D 61 ILE cc_start: 0.5275 (mm) cc_final: 0.4737 (tt) REVERT: D 290 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: D 350 MET cc_start: 0.8588 (ppp) cc_final: 0.8382 (ppp) REVERT: E 199 MET cc_start: -0.0636 (mmt) cc_final: -0.0890 (mmt) REVERT: E 267 LEU cc_start: 0.9383 (mt) cc_final: 0.9144 (pp) REVERT: E 350 MET cc_start: 0.9318 (tmm) cc_final: 0.8923 (ppp) REVERT: G 207 MET cc_start: 0.7984 (ttm) cc_final: 0.7419 (mtp) REVERT: H 278 LEU cc_start: 0.8986 (tp) cc_final: 0.8712 (tt) outliers start: 47 outliers final: 40 residues processed: 164 average time/residue: 0.3225 time to fit residues: 87.2636 Evaluate side-chains 167 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain 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 128 THR Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 233 LEU 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 160 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 278 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 268 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 301 MET 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 G residue 353 ARG 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 268 GLU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 288 PHE Chi-restraints excluded: chain H residue 353 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 198 optimal weight: 0.0030 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 221 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** 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 = 0.4521 r_free = 0.4521 target = 0.137691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.102979 restraints weight = 60164.072| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 4.41 r_work: 0.3722 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2032 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= 0.171 Angle : 0.630 14.811 29192 Z= 0.300 Chirality : 0.040 0.250 3488 Planarity : 0.004 0.048 3840 Dihedral : 4.220 30.583 3088 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.94 % Allowed : 16.72 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2752 helix: 1.32 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.29 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 351 HIS 0.017 0.001 HIS A 319 PHE 0.032 0.001 PHE F 288 TYR 0.032 0.001 TYR H 173 ARG 0.005 0.000 ARG D 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.30 seconds wall clock time: 76 minutes 58.85 seconds (4618.85 seconds total)