Starting phenix.real_space_refine on Sat Aug 23 02:01:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nd1_0440/08_2025/6nd1_0440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nd1_0440/08_2025/6nd1_0440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nd1_0440/08_2025/6nd1_0440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nd1_0440/08_2025/6nd1_0440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nd1_0440/08_2025/6nd1_0440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nd1_0440/08_2025/6nd1_0440.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 36 5.16 5 C 5990 2.51 5 N 1514 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9186 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3031 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 17, 'TRANS': 372} Chain breaks: 5 Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3565 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 3, 'TYR:plan': 2, 'ASP:plan': 1, 'TRP:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "D" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 270 Classifications: {'peptide': 41} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Chain: "F" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 734 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU A 284 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU A 284 " occ=0.75 residue: pdb=" N GLY A 316 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY A 316 " occ=0.88 residue: pdb=" N LEU A 398 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU A 398 " occ=0.75 residue: pdb=" N ALA A 413 " occ=0.88 ... (3 atoms not shown) pdb=" CB ALA A 413 " occ=0.88 Time building chain proxies: 2.02, per 1000 atoms: 0.22 Number of scatterers: 9186 At special positions: 0 Unit cell: (108, 106.65, 121.5, 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 36 16.00 O 1646 8.00 N 1514 7.00 C 5990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 292.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 65.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 28 through 48 removed outlier: 3.743A pdb=" N ILE B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N MET B 69 " --> pdb=" O TRP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.731A pdb=" N ILE B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 146 through 174 removed outlier: 4.015A pdb=" N CYS B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 197 removed outlier: 3.878A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 184 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 223 removed outlier: 3.998A pdb=" N LEU B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 238 removed outlier: 4.208A pdb=" N VAL B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 removed outlier: 4.016A pdb=" N ALA B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 289 removed outlier: 3.722A pdb=" N SER B 289 " --> pdb=" O PHE B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 290 through 314 removed outlier: 3.707A pdb=" N MET B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 384 removed outlier: 4.000A pdb=" N THR B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.170A pdb=" N LYS B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 440 removed outlier: 3.870A pdb=" N LYS B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 417 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.628A pdb=" N ASP B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.595A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 454 " --> pdb=" O MET B 450 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.027A pdb=" N THR A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.385A pdb=" N GLU A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.590A pdb=" N PHE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 110 Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.541A pdb=" N VAL A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.678A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.861A pdb=" N ASN A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.828A pdb=" N ILE A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.794A pdb=" N GLU A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.893A pdb=" N LEU A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.855A pdb=" N PHE A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.100A pdb=" N LEU A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 373 " --> pdb=" O CYS A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.616A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 486 through 494 removed outlier: 3.986A pdb=" N ALA A 489 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.523A pdb=" N TYR C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.682A pdb=" N TYR C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.767A pdb=" N ALA D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 75 removed outlier: 3.818A pdb=" N PHE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 60 removed outlier: 4.378A pdb=" N LEU E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 81 removed outlier: 4.198A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 78 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET E 81 " --> pdb=" O GLN E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 124 Proline residue: E 115 - end of helix removed outlier: 3.862A pdb=" N GLY E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 153 removed outlier: 3.680A pdb=" N TRP E 131 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 149 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 4.282A pdb=" N VAL E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS E 167 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS E 168 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU E 169 " --> pdb=" O MET E 165 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 174 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 122 through 136 removed outlier: 3.792A pdb=" N LEU F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 131 " --> pdb=" O GLN F 127 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 152 removed outlier: 4.120A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 175 through 192 removed outlier: 3.629A pdb=" N LEU F 179 " --> pdb=" O LYS F 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 203 removed outlier: 5.832A pdb=" N THR B 201 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 212 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU B 210 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 436 removed outlier: 3.969A pdb=" N LYS A 432 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.575A pdb=" N LYS A 524 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.575A pdb=" N LYS A 524 " --> pdb=" O SER A 519 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1473 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: 1.18 Time building geometry restraints manager: 1.17 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: 2687 1.34 - 1.46: 1685 1.46 - 1.58: 4938 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 9366 Sorted by residual: bond pdb=" C THR B 379 " pdb=" N TRP B 380 " ideal model delta sigma weight residual 1.335 1.226 0.110 1.38e-02 5.25e+03 6.30e+01 bond pdb=" C TRP A 566 " pdb=" N GLU A 567 " ideal model delta sigma weight residual 1.331 1.238 0.093 1.37e-02 5.33e+03 4.61e+01 bond pdb=" C GLY A 576 " pdb=" N GLN A 577 " ideal model delta sigma weight residual 1.331 1.221 0.110 2.07e-02 2.33e+03 2.83e+01 bond pdb=" C GLN B 398 " pdb=" N GLY B 399 " ideal model delta sigma weight residual 1.330 1.258 0.072 1.42e-02 4.96e+03 2.56e+01 bond pdb=" N ILE C 79 " pdb=" CA ILE C 79 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.10e+00 ... (remaining 9361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 12522 4.03 - 8.06: 127 8.06 - 12.09: 30 12.09 - 16.11: 3 16.11 - 20.14: 3 Bond angle restraints: 12685 Sorted by residual: angle pdb=" C ILE C 75 " pdb=" CA ILE C 75 " pdb=" CB ILE C 75 " ideal model delta sigma weight residual 112.14 129.12 -16.98 1.35e+00 5.49e-01 1.58e+02 angle pdb=" C GLU F 124 " pdb=" CA GLU F 124 " pdb=" CB GLU F 124 " ideal model delta sigma weight residual 110.85 130.99 -20.14 1.70e+00 3.46e-01 1.40e+02 angle pdb=" C ALA B 463 " pdb=" CA ALA B 463 " pdb=" CB ALA B 463 " ideal model delta sigma weight residual 110.68 125.60 -14.92 1.70e+00 3.46e-01 7.70e+01 angle pdb=" C GLU A 440 " pdb=" CA GLU A 440 " pdb=" CB GLU A 440 " ideal model delta sigma weight residual 110.45 91.69 18.76 2.15e+00 2.16e-01 7.61e+01 angle pdb=" C PHE B 218 " pdb=" CA PHE B 218 " pdb=" CB PHE B 218 " ideal model delta sigma weight residual 109.56 123.30 -13.74 1.65e+00 3.67e-01 6.94e+01 ... (remaining 12680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 4902 17.48 - 34.95: 569 34.95 - 52.43: 124 52.43 - 69.91: 28 69.91 - 87.39: 14 Dihedral angle restraints: 5637 sinusoidal: 2211 harmonic: 3426 Sorted by residual: dihedral pdb=" C GLU A 440 " pdb=" N GLU A 440 " pdb=" CA GLU A 440 " pdb=" CB GLU A 440 " ideal model delta harmonic sigma weight residual -122.60 -100.10 -22.50 0 2.50e+00 1.60e-01 8.10e+01 dihedral pdb=" C GLU F 124 " pdb=" N GLU F 124 " pdb=" CA GLU F 124 " pdb=" CB GLU F 124 " ideal model delta harmonic sigma weight residual -122.60 -143.24 20.64 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" CA PRO B 62 " pdb=" C PRO B 62 " pdb=" N LEU B 63 " pdb=" CA LEU B 63 " ideal model delta harmonic sigma weight residual 180.00 140.65 39.35 0 5.00e+00 4.00e-02 6.19e+01 ... (remaining 5634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1385 0.131 - 0.261: 89 0.261 - 0.392: 11 0.392 - 0.523: 6 0.523 - 0.654: 2 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA GLU F 124 " pdb=" N GLU F 124 " pdb=" C GLU F 124 " pdb=" CB GLU F 124 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA PHE B 236 " pdb=" N PHE B 236 " pdb=" C PHE B 236 " pdb=" CB PHE B 236 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ALA B 462 " pdb=" N ALA B 462 " pdb=" C ALA B 462 " pdb=" CB ALA B 462 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.52 2.00e-01 2.50e+01 6.80e+00 ... (remaining 1490 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 444 " -0.059 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO A 445 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 265 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C TYR B 265 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR B 265 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B 266 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 160 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C VAL E 160 " 0.053 2.00e-02 2.50e+03 pdb=" O VAL E 160 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN E 161 " -0.018 2.00e-02 2.50e+03 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2168 2.78 - 3.31: 8588 3.31 - 3.84: 14120 3.84 - 4.37: 15051 4.37 - 4.90: 26046 Nonbonded interactions: 65973 Sorted by model distance: nonbonded pdb=" OG1 THR A 599 " pdb=" N THR A 600 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR A 444 " pdb=" OG SER A 447 " model vdw 2.287 3.040 nonbonded pdb=" O HIS A 390 " pdb=" OH TYR F 190 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 483 " pdb=" OG SER A 483 " model vdw 2.301 3.040 nonbonded pdb=" O ASN B 290 " pdb=" OD1 ASN B 290 " model vdw 2.302 3.040 ... (remaining 65968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.009 0.110 9366 Z= 0.441 Angle : 1.231 20.144 12685 Z= 0.718 Chirality : 0.079 0.654 1493 Planarity : 0.009 0.090 1586 Dihedral : 16.242 87.386 3409 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 0.10 % Allowed : 15.61 % Favored : 84.29 % Cbeta Deviations : 1.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.89 (0.20), residues: 1145 helix: -2.28 (0.15), residues: 689 sheet: -2.93 (0.45), residues: 80 loop : -2.70 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 509 TYR 0.030 0.002 TYR B 287 PHE 0.041 0.003 PHE E 66 TRP 0.021 0.003 TRP A 242 HIS 0.011 0.002 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00919 ( 9366) covalent geometry : angle 1.23096 (12685) hydrogen bonds : bond 0.15592 ( 505) hydrogen bonds : angle 6.72425 ( 1473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.5483 (tttt) cc_final: 0.4969 (tttt) REVERT: B 237 TYR cc_start: 0.7040 (m-80) cc_final: 0.6619 (m-80) REVERT: B 238 ARG cc_start: 0.7011 (mmm160) cc_final: 0.5533 (mmm160) REVERT: B 400 MET cc_start: 0.8025 (mtt) cc_final: 0.7735 (mtm) REVERT: B 406 ARG cc_start: 0.7122 (mpt-90) cc_final: 0.6734 (mpt-90) REVERT: A 359 ILE cc_start: 0.9160 (mm) cc_final: 0.8940 (mp) REVERT: A 431 ILE cc_start: 0.8864 (mt) cc_final: 0.8610 (mm) REVERT: A 473 GLU cc_start: 0.7963 (tp30) cc_final: 0.7537 (tp30) REVERT: A 491 MET cc_start: 0.8933 (mtp) cc_final: 0.8639 (mtp) REVERT: A 521 LYS cc_start: 0.9150 (tptm) cc_final: 0.8519 (ttmt) REVERT: A 562 ASP cc_start: 0.6913 (p0) cc_final: 0.6705 (p0) REVERT: C 49 LYS cc_start: 0.8446 (tttp) cc_final: 0.8129 (tttt) REVERT: E 46 MET cc_start: 0.6966 (ttm) cc_final: 0.6523 (tmm) REVERT: E 54 LYS cc_start: 0.7560 (tttt) cc_final: 0.7030 (tmtt) REVERT: E 99 ARG cc_start: 0.6868 (ttp-170) cc_final: 0.6605 (mmm-85) REVERT: E 165 MET cc_start: 0.6274 (mmm) cc_final: 0.6073 (mmp) REVERT: F 152 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8334 (mmmt) REVERT: F 158 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F 182 GLU cc_start: 0.7656 (tp30) cc_final: 0.7260 (tp30) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.0931 time to fit residues: 31.2724 Evaluate side-chains 192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0000 chunk 100 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 220 HIS B 261 GLN B 347 GLN B 403 ASN A 55 ASN A 255 HIS A 261 ASN A 307 GLN A 334 HIS A 376 ASN A 427 ASN A 494 GLN F 106 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114212 restraints weight = 17385.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116357 restraints weight = 11829.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117815 restraints weight = 9226.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118604 restraints weight = 7861.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119192 restraints weight = 7141.347| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9366 Z= 0.131 Angle : 0.635 9.422 12685 Z= 0.323 Chirality : 0.043 0.156 1493 Planarity : 0.005 0.066 1586 Dihedral : 5.381 70.446 1242 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.23), residues: 1145 helix: -0.48 (0.18), residues: 720 sheet: -2.27 (0.50), residues: 77 loop : -2.26 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 105 TYR 0.018 0.001 TYR B 344 PHE 0.023 0.001 PHE E 66 TRP 0.025 0.002 TRP B 65 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9366) covalent geometry : angle 0.63469 (12685) hydrogen bonds : bond 0.04194 ( 505) hydrogen bonds : angle 4.28011 ( 1473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 254 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.5307 (tttt) cc_final: 0.4876 (tttt) REVERT: B 131 LEU cc_start: 0.8812 (tp) cc_final: 0.8558 (tp) REVERT: B 238 ARG cc_start: 0.6582 (mmm160) cc_final: 0.5459 (mmm160) REVERT: B 261 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8300 (mm-40) REVERT: B 400 MET cc_start: 0.7830 (mtt) cc_final: 0.7535 (mtm) REVERT: B 406 ARG cc_start: 0.7142 (mpt-90) cc_final: 0.6673 (mpt-90) REVERT: B 439 LEU cc_start: 0.9302 (tt) cc_final: 0.8685 (mt) REVERT: A 336 LEU cc_start: 0.8863 (tp) cc_final: 0.8422 (tt) REVERT: A 376 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8245 (m110) REVERT: A 431 ILE cc_start: 0.8796 (mt) cc_final: 0.8495 (mm) REVERT: A 521 LYS cc_start: 0.9038 (tptm) cc_final: 0.8331 (ttmt) REVERT: A 562 ASP cc_start: 0.6104 (p0) cc_final: 0.5573 (p0) REVERT: A 567 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 601 ASP cc_start: 0.7918 (m-30) cc_final: 0.7639 (m-30) REVERT: E 46 MET cc_start: 0.6929 (ttm) cc_final: 0.6458 (tmm) REVERT: E 54 LYS cc_start: 0.7736 (tttt) cc_final: 0.7227 (tmtt) REVERT: E 99 ARG cc_start: 0.6830 (ttp-170) cc_final: 0.6380 (mmm-85) REVERT: E 103 SER cc_start: 0.8805 (p) cc_final: 0.8458 (p) REVERT: E 165 MET cc_start: 0.6317 (mmm) cc_final: 0.5516 (mpp) REVERT: F 110 ARG cc_start: 0.6418 (tmm-80) cc_final: 0.6198 (tmm-80) REVERT: F 152 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8310 (mmmt) REVERT: F 182 GLU cc_start: 0.7708 (tp30) cc_final: 0.7334 (tp30) outliers start: 4 outliers final: 1 residues processed: 257 average time/residue: 0.0831 time to fit residues: 29.9822 Evaluate side-chains 204 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 330 HIS A 361 GLN A 427 ASN E 69 ASN E 72 HIS F 139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111157 restraints weight = 17476.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113209 restraints weight = 12064.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114349 restraints weight = 9458.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115358 restraints weight = 8196.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115717 restraints weight = 7433.118| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9366 Z= 0.183 Angle : 0.651 9.234 12685 Z= 0.329 Chirality : 0.044 0.191 1493 Planarity : 0.005 0.057 1586 Dihedral : 5.059 59.332 1242 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.10 % Allowed : 5.51 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.24), residues: 1145 helix: 0.09 (0.19), residues: 727 sheet: -1.89 (0.53), residues: 75 loop : -2.12 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 106 TYR 0.020 0.001 TYR B 344 PHE 0.017 0.002 PHE E 66 TRP 0.017 0.002 TRP B 65 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9366) covalent geometry : angle 0.65054 (12685) hydrogen bonds : bond 0.04200 ( 505) hydrogen bonds : angle 4.26559 ( 1473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 LYS cc_start: 0.5344 (tttt) cc_final: 0.4935 (tttt) REVERT: B 238 ARG cc_start: 0.6794 (mmm160) cc_final: 0.5451 (mmm160) REVERT: B 347 GLN cc_start: 0.7284 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 400 MET cc_start: 0.7866 (mtt) cc_final: 0.7553 (mtm) REVERT: B 406 ARG cc_start: 0.7237 (mpt-90) cc_final: 0.6730 (mpt-90) REVERT: A 248 SER cc_start: 0.9246 (p) cc_final: 0.9016 (t) REVERT: A 325 ILE cc_start: 0.8933 (mm) cc_final: 0.8379 (mt) REVERT: A 431 ILE cc_start: 0.8810 (mt) cc_final: 0.8492 (mm) REVERT: A 490 MET cc_start: 0.7214 (tmm) cc_final: 0.7014 (tmm) REVERT: A 521 LYS cc_start: 0.8966 (tptm) cc_final: 0.8291 (ttmt) REVERT: A 562 ASP cc_start: 0.6336 (p0) cc_final: 0.6112 (p0) REVERT: A 567 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 601 ASP cc_start: 0.8136 (m-30) cc_final: 0.7847 (m-30) REVERT: E 46 MET cc_start: 0.6955 (ttm) cc_final: 0.6473 (tmm) REVERT: E 54 LYS cc_start: 0.7610 (tttt) cc_final: 0.7157 (tmtt) REVERT: E 99 ARG cc_start: 0.6679 (ttp-170) cc_final: 0.6293 (mmm-85) REVERT: E 103 SER cc_start: 0.8770 (p) cc_final: 0.8561 (p) REVERT: E 165 MET cc_start: 0.6408 (mmm) cc_final: 0.5623 (mpp) REVERT: F 152 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8292 (mmmt) REVERT: F 154 ARG cc_start: 0.7329 (mtp180) cc_final: 0.6284 (ttp80) REVERT: F 182 GLU cc_start: 0.7743 (tp30) cc_final: 0.7391 (tp30) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.0807 time to fit residues: 26.5825 Evaluate side-chains 192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN D 72 HIS E 123 ASN F 139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115578 restraints weight = 17186.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117793 restraints weight = 11369.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118867 restraints weight = 8684.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120189 restraints weight = 7465.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120697 restraints weight = 6594.231| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9366 Z= 0.125 Angle : 0.606 10.774 12685 Z= 0.302 Chirality : 0.043 0.215 1493 Planarity : 0.004 0.057 1586 Dihedral : 4.741 57.222 1242 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.25), residues: 1145 helix: 0.51 (0.19), residues: 716 sheet: -1.50 (0.57), residues: 77 loop : -1.68 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 106 TYR 0.025 0.001 TYR B 287 PHE 0.035 0.001 PHE B 236 TRP 0.013 0.001 TRP B 35 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9366) covalent geometry : angle 0.60630 (12685) hydrogen bonds : bond 0.03670 ( 505) hydrogen bonds : angle 3.88835 ( 1473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: B 48 GLN cc_start: 0.8407 (mm110) cc_final: 0.7873 (mp10) REVERT: B 61 ASP cc_start: 0.6338 (p0) cc_final: 0.6137 (p0) REVERT: B 238 ARG cc_start: 0.6691 (mmm160) cc_final: 0.5430 (mmm160) REVERT: B 249 MET cc_start: 0.8449 (mmm) cc_final: 0.8079 (mmm) REVERT: B 291 THR cc_start: 0.6515 (p) cc_final: 0.6279 (t) REVERT: B 347 GLN cc_start: 0.7418 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 377 SER cc_start: 0.8457 (m) cc_final: 0.8217 (t) REVERT: B 400 MET cc_start: 0.7871 (mtt) cc_final: 0.7572 (mtm) REVERT: B 406 ARG cc_start: 0.7124 (mpt-90) cc_final: 0.6664 (mpt-90) REVERT: A 248 SER cc_start: 0.9215 (p) cc_final: 0.8966 (t) REVERT: A 336 LEU cc_start: 0.8722 (tp) cc_final: 0.8376 (tt) REVERT: A 402 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8471 (mmmt) REVERT: A 431 ILE cc_start: 0.8822 (mt) cc_final: 0.8482 (mm) REVERT: A 521 LYS cc_start: 0.8951 (tptm) cc_final: 0.8341 (ttmt) REVERT: A 567 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7819 (mm-30) REVERT: A 601 ASP cc_start: 0.7959 (m-30) cc_final: 0.7692 (m-30) REVERT: A 606 MET cc_start: 0.8984 (mtm) cc_final: 0.8589 (mtp) REVERT: E 46 MET cc_start: 0.7006 (ttm) cc_final: 0.6439 (tmm) REVERT: E 54 LYS cc_start: 0.7887 (tttt) cc_final: 0.7356 (tmtt) REVERT: E 97 LEU cc_start: 0.7861 (mt) cc_final: 0.7578 (mt) REVERT: E 103 SER cc_start: 0.8743 (p) cc_final: 0.8517 (p) REVERT: E 128 GLU cc_start: 0.7646 (tp30) cc_final: 0.7332 (tp30) REVERT: E 159 TRP cc_start: 0.6991 (t-100) cc_final: 0.6764 (t-100) REVERT: E 165 MET cc_start: 0.6168 (mmm) cc_final: 0.5349 (mpp) REVERT: F 154 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6205 (ttp80) REVERT: F 182 GLU cc_start: 0.7691 (tp30) cc_final: 0.7425 (tp30) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0755 time to fit residues: 25.3886 Evaluate side-chains 202 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN F 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111738 restraints weight = 16768.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113824 restraints weight = 11452.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115021 restraints weight = 8876.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115941 restraints weight = 7627.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116622 restraints weight = 6851.137| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9366 Z= 0.128 Angle : 0.594 10.624 12685 Z= 0.297 Chirality : 0.043 0.192 1493 Planarity : 0.004 0.059 1586 Dihedral : 4.599 54.952 1242 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.25), residues: 1145 helix: 0.74 (0.19), residues: 719 sheet: -1.35 (0.58), residues: 75 loop : -1.52 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.015 0.001 TYR B 344 PHE 0.013 0.001 PHE B 236 TRP 0.019 0.002 TRP B 35 HIS 0.003 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9366) covalent geometry : angle 0.59442 (12685) hydrogen bonds : bond 0.03513 ( 505) hydrogen bonds : angle 3.79496 ( 1473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 61 ASP cc_start: 0.6068 (p0) cc_final: 0.5813 (p0) REVERT: B 238 ARG cc_start: 0.6695 (mmm160) cc_final: 0.5351 (mmm160) REVERT: B 249 MET cc_start: 0.8575 (mmm) cc_final: 0.8160 (mmm) REVERT: B 347 GLN cc_start: 0.7251 (tm-30) cc_final: 0.7018 (tm-30) REVERT: B 400 MET cc_start: 0.7902 (mtt) cc_final: 0.7682 (mtt) REVERT: B 406 ARG cc_start: 0.7231 (mpt-90) cc_final: 0.6708 (mpt-90) REVERT: A 248 SER cc_start: 0.9194 (p) cc_final: 0.8970 (t) REVERT: A 402 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8499 (mmmt) REVERT: A 431 ILE cc_start: 0.8957 (mt) cc_final: 0.8629 (mm) REVERT: A 521 LYS cc_start: 0.8843 (tptm) cc_final: 0.8278 (ttpt) REVERT: A 562 ASP cc_start: 0.6559 (p0) cc_final: 0.5859 (p0) REVERT: A 567 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 601 ASP cc_start: 0.7812 (m-30) cc_final: 0.7534 (m-30) REVERT: E 46 MET cc_start: 0.7046 (ttm) cc_final: 0.6410 (tmm) REVERT: E 54 LYS cc_start: 0.7888 (tttt) cc_final: 0.7384 (tmtt) REVERT: E 165 MET cc_start: 0.5981 (mmm) cc_final: 0.5279 (mpp) REVERT: F 154 ARG cc_start: 0.7204 (mtp180) cc_final: 0.6389 (ttp80) REVERT: F 182 GLU cc_start: 0.7751 (tp30) cc_final: 0.7386 (tp30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0800 time to fit residues: 25.4371 Evaluate side-chains 193 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 30.0000 chunk 86 optimal weight: 0.0170 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 220 HIS ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113747 restraints weight = 16722.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115883 restraints weight = 11273.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117345 restraints weight = 8658.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117733 restraints weight = 7302.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118616 restraints weight = 6798.437| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9366 Z= 0.116 Angle : 0.591 10.536 12685 Z= 0.292 Chirality : 0.042 0.181 1493 Planarity : 0.004 0.059 1586 Dihedral : 4.458 54.018 1242 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.26), residues: 1145 helix: 0.92 (0.19), residues: 719 sheet: -1.20 (0.59), residues: 75 loop : -1.37 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 412 TYR 0.012 0.001 TYR B 344 PHE 0.013 0.001 PHE E 66 TRP 0.015 0.001 TRP A 242 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9366) covalent geometry : angle 0.59065 (12685) hydrogen bonds : bond 0.03353 ( 505) hydrogen bonds : angle 3.66233 ( 1473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 61 ASP cc_start: 0.6480 (p0) cc_final: 0.6205 (p0) REVERT: B 238 ARG cc_start: 0.6647 (mmm160) cc_final: 0.5373 (mmm160) REVERT: B 347 GLN cc_start: 0.7265 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 377 SER cc_start: 0.8524 (m) cc_final: 0.8185 (t) REVERT: B 400 MET cc_start: 0.7895 (mtt) cc_final: 0.7680 (mtt) REVERT: B 406 ARG cc_start: 0.7173 (mpt-90) cc_final: 0.6684 (mpt-90) REVERT: A 248 SER cc_start: 0.9140 (p) cc_final: 0.8936 (t) REVERT: A 279 LEU cc_start: 0.8711 (tp) cc_final: 0.8490 (tp) REVERT: A 336 LEU cc_start: 0.8689 (tp) cc_final: 0.8354 (tt) REVERT: A 431 ILE cc_start: 0.8817 (mt) cc_final: 0.8522 (mm) REVERT: A 521 LYS cc_start: 0.8827 (tptm) cc_final: 0.8224 (ttpt) REVERT: A 562 ASP cc_start: 0.6483 (p0) cc_final: 0.5848 (p0) REVERT: A 601 ASP cc_start: 0.7699 (m-30) cc_final: 0.7374 (m-30) REVERT: E 46 MET cc_start: 0.7136 (ttm) cc_final: 0.6300 (tmm) REVERT: E 54 LYS cc_start: 0.7752 (tttt) cc_final: 0.7308 (tmtt) REVERT: E 165 MET cc_start: 0.5660 (mmm) cc_final: 0.5168 (mpp) REVERT: F 182 GLU cc_start: 0.7765 (tp30) cc_final: 0.7402 (tp30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.0723 time to fit residues: 24.2817 Evaluate side-chains 195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 46 optimal weight: 0.0170 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.6034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN D 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111336 restraints weight = 16910.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113497 restraints weight = 11385.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114779 restraints weight = 8759.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115809 restraints weight = 7447.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116446 restraints weight = 6681.531| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9366 Z= 0.132 Angle : 0.620 10.758 12685 Z= 0.307 Chirality : 0.044 0.205 1493 Planarity : 0.005 0.091 1586 Dihedral : 4.448 52.824 1242 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.10 % Allowed : 2.04 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 1145 helix: 0.94 (0.19), residues: 713 sheet: -1.18 (0.59), residues: 75 loop : -1.28 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.023 0.001 TYR B 287 PHE 0.013 0.001 PHE E 66 TRP 0.017 0.002 TRP B 35 HIS 0.003 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9366) covalent geometry : angle 0.61984 (12685) hydrogen bonds : bond 0.03452 ( 505) hydrogen bonds : angle 3.78987 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 61 ASP cc_start: 0.6399 (p0) cc_final: 0.6140 (p0) REVERT: B 238 ARG cc_start: 0.6656 (mmm160) cc_final: 0.5329 (mmm160) REVERT: B 249 MET cc_start: 0.8559 (mmm) cc_final: 0.8050 (mmm) REVERT: B 294 MET cc_start: 0.5717 (tpp) cc_final: 0.5203 (tpt) REVERT: B 347 GLN cc_start: 0.7282 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 400 MET cc_start: 0.7905 (mtt) cc_final: 0.7695 (mtt) REVERT: B 406 ARG cc_start: 0.7194 (mpt-90) cc_final: 0.6727 (mpt-90) REVERT: B 439 LEU cc_start: 0.9303 (tt) cc_final: 0.8227 (tt) REVERT: A 248 SER cc_start: 0.9155 (p) cc_final: 0.8949 (t) REVERT: A 279 LEU cc_start: 0.8760 (tp) cc_final: 0.8526 (tp) REVERT: A 521 LYS cc_start: 0.8838 (tptm) cc_final: 0.8271 (ttpt) REVERT: A 562 ASP cc_start: 0.6522 (p0) cc_final: 0.5940 (p0) REVERT: A 601 ASP cc_start: 0.7636 (m-30) cc_final: 0.7338 (m-30) REVERT: A 606 MET cc_start: 0.9074 (mtm) cc_final: 0.8739 (mtp) REVERT: E 46 MET cc_start: 0.7112 (ttm) cc_final: 0.6277 (tmm) REVERT: E 54 LYS cc_start: 0.7956 (tttt) cc_final: 0.7452 (tmtt) REVERT: E 75 TYR cc_start: 0.7607 (t80) cc_final: 0.7344 (t80) REVERT: E 99 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7836 (mmm-85) REVERT: E 105 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7524 (ptt90) REVERT: E 165 MET cc_start: 0.6109 (mmm) cc_final: 0.5763 (mpp) REVERT: F 154 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.6373 (ttp80) REVERT: F 182 GLU cc_start: 0.7843 (tp30) cc_final: 0.7550 (tp30) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.0740 time to fit residues: 25.0086 Evaluate side-chains 196 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112895 restraints weight = 16932.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115093 restraints weight = 11217.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116410 restraints weight = 8582.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117541 restraints weight = 7270.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118079 restraints weight = 6477.339| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9366 Z= 0.119 Angle : 0.615 10.736 12685 Z= 0.300 Chirality : 0.043 0.172 1493 Planarity : 0.004 0.077 1586 Dihedral : 4.372 52.635 1242 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.25), residues: 1145 helix: 1.03 (0.19), residues: 714 sheet: -1.13 (0.59), residues: 75 loop : -1.22 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.013 0.001 TYR B 287 PHE 0.014 0.001 PHE E 66 TRP 0.011 0.001 TRP E 159 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9366) covalent geometry : angle 0.61469 (12685) hydrogen bonds : bond 0.03347 ( 505) hydrogen bonds : angle 3.69112 ( 1473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ASP cc_start: 0.6649 (p0) cc_final: 0.6299 (p0) REVERT: B 85 ILE cc_start: 0.8884 (pt) cc_final: 0.8562 (tp) REVERT: B 238 ARG cc_start: 0.6596 (mmm160) cc_final: 0.5492 (mmm160) REVERT: B 249 MET cc_start: 0.8480 (mmm) cc_final: 0.8147 (mmm) REVERT: B 294 MET cc_start: 0.5903 (tpp) cc_final: 0.5429 (tpt) REVERT: B 347 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6983 (tm-30) REVERT: B 400 MET cc_start: 0.7905 (mtt) cc_final: 0.7329 (mtm) REVERT: B 406 ARG cc_start: 0.7203 (mpt-90) cc_final: 0.6715 (mpt-90) REVERT: B 439 LEU cc_start: 0.9301 (tt) cc_final: 0.8164 (tt) REVERT: A 279 LEU cc_start: 0.8723 (tp) cc_final: 0.8483 (tp) REVERT: A 336 LEU cc_start: 0.8741 (tp) cc_final: 0.8407 (tt) REVERT: A 521 LYS cc_start: 0.8844 (tptm) cc_final: 0.8293 (ttpt) REVERT: A 562 ASP cc_start: 0.6478 (p0) cc_final: 0.5904 (p0) REVERT: A 567 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7420 (mm-30) REVERT: A 601 ASP cc_start: 0.7625 (m-30) cc_final: 0.7313 (m-30) REVERT: A 606 MET cc_start: 0.9101 (mtm) cc_final: 0.8811 (mtp) REVERT: E 46 MET cc_start: 0.7105 (ttm) cc_final: 0.6260 (tmm) REVERT: E 54 LYS cc_start: 0.7746 (tttt) cc_final: 0.7314 (tmtt) REVERT: E 75 TYR cc_start: 0.7598 (t80) cc_final: 0.7321 (t80) REVERT: E 97 LEU cc_start: 0.7890 (mm) cc_final: 0.7667 (mm) REVERT: E 105 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7375 (ptt90) REVERT: E 165 MET cc_start: 0.6070 (mmm) cc_final: 0.5758 (mpp) REVERT: F 154 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.6383 (ttp80) REVERT: F 182 GLU cc_start: 0.8028 (tp30) cc_final: 0.7616 (tp30) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.0739 time to fit residues: 24.2809 Evaluate side-chains 194 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 0.0570 chunk 5 optimal weight: 0.0050 chunk 52 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116072 restraints weight = 16932.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118398 restraints weight = 11121.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119954 restraints weight = 8417.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120827 restraints weight = 7036.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121582 restraints weight = 6312.148| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9366 Z= 0.109 Angle : 0.605 9.919 12685 Z= 0.295 Chirality : 0.043 0.168 1493 Planarity : 0.004 0.070 1586 Dihedral : 4.185 51.422 1242 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1145 helix: 1.15 (0.19), residues: 713 sheet: -1.13 (0.58), residues: 77 loop : -1.07 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 160 TYR 0.010 0.001 TYR B 344 PHE 0.015 0.001 PHE E 66 TRP 0.011 0.001 TRP E 159 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9366) covalent geometry : angle 0.60452 (12685) hydrogen bonds : bond 0.03092 ( 505) hydrogen bonds : angle 3.55213 ( 1473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: B 61 ASP cc_start: 0.6750 (p0) cc_final: 0.6431 (p0) REVERT: B 85 ILE cc_start: 0.8914 (pt) cc_final: 0.8620 (tp) REVERT: B 238 ARG cc_start: 0.6498 (mmm160) cc_final: 0.5438 (mmm160) REVERT: B 249 MET cc_start: 0.8326 (mmm) cc_final: 0.8000 (mmm) REVERT: B 347 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6920 (tm-30) REVERT: B 380 TRP cc_start: 0.8729 (t-100) cc_final: 0.8173 (t-100) REVERT: B 406 ARG cc_start: 0.7237 (mpt-90) cc_final: 0.6763 (mpt-90) REVERT: B 439 LEU cc_start: 0.9250 (tt) cc_final: 0.8122 (tt) REVERT: A 279 LEU cc_start: 0.8561 (tp) cc_final: 0.8339 (tp) REVERT: A 562 ASP cc_start: 0.6463 (p0) cc_final: 0.5924 (p0) REVERT: A 567 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 606 MET cc_start: 0.9010 (mtm) cc_final: 0.8661 (mtp) REVERT: E 46 MET cc_start: 0.7079 (ttm) cc_final: 0.6207 (tmm) REVERT: E 54 LYS cc_start: 0.7803 (tttt) cc_final: 0.7385 (tmtt) REVERT: E 165 MET cc_start: 0.6094 (mmm) cc_final: 0.5880 (mpp) REVERT: F 144 VAL cc_start: 0.8602 (t) cc_final: 0.8341 (m) REVERT: F 154 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.6440 (ttp80) REVERT: F 182 GLU cc_start: 0.7980 (tp30) cc_final: 0.7556 (tp30) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.0657 time to fit residues: 22.4236 Evaluate side-chains 196 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2733 > 50: distance: 27 - 62: 30.877 distance: 30 - 59: 35.518 distance: 55 - 59: 35.329 distance: 59 - 60: 42.274 distance: 60 - 61: 46.340 distance: 60 - 63: 27.499 distance: 61 - 62: 47.445 distance: 61 - 67: 40.080 distance: 63 - 64: 43.146 distance: 63 - 65: 38.841 distance: 64 - 66: 43.061 distance: 67 - 68: 51.263 distance: 67 - 73: 43.618 distance: 68 - 69: 35.168 distance: 68 - 71: 32.975 distance: 69 - 70: 33.702 distance: 69 - 74: 32.376 distance: 71 - 72: 52.390 distance: 72 - 73: 16.517 distance: 75 - 76: 43.728 distance: 75 - 78: 45.250 distance: 76 - 77: 24.035 distance: 76 - 82: 46.296 distance: 78 - 79: 42.513 distance: 79 - 80: 19.983 distance: 79 - 81: 25.857 distance: 82 - 83: 35.825 distance: 83 - 84: 34.483 distance: 84 - 85: 55.840 distance: 84 - 86: 5.735 distance: 88 - 95: 69.799 distance: 90 - 91: 50.236 distance: 91 - 92: 39.662 distance: 92 - 93: 39.268 distance: 92 - 94: 41.937 distance: 95 - 96: 30.735 distance: 95 - 101: 40.879 distance: 96 - 97: 40.380 distance: 96 - 99: 49.159 distance: 97 - 98: 56.459 distance: 100 - 101: 55.280 distance: 102 - 103: 21.445 distance: 103 - 104: 33.496 distance: 103 - 106: 45.069 distance: 104 - 105: 27.634 distance: 104 - 107: 41.373 distance: 107 - 108: 57.537 distance: 107 - 113: 7.010 distance: 108 - 111: 39.446 distance: 111 - 112: 53.099 distance: 112 - 113: 33.747 distance: 114 - 115: 41.331 distance: 115 - 118: 38.710 distance: 116 - 117: 56.313 distance: 116 - 123: 26.293 distance: 118 - 119: 47.827 distance: 119 - 120: 27.470 distance: 120 - 122: 19.657 distance: 123 - 124: 27.348 distance: 124 - 125: 17.780 distance: 124 - 127: 56.248 distance: 125 - 126: 19.999 distance: 125 - 130: 28.651 distance: 127 - 128: 55.322 distance: 127 - 129: 39.876