Starting phenix.real_space_refine on Sat Dec 9 00:35:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/12_2023/6xwr_10636.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/12_2023/6xwr_10636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/12_2023/6xwr_10636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/12_2023/6xwr_10636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/12_2023/6xwr_10636.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/12_2023/6xwr_10636.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 48 5.16 5 C 6309 2.51 5 N 1551 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 376": "OD1" <-> "OD2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C GLU 420": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9564 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Chain: "B" Number of atoms: 3187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3227 Chain: "C" Number of atoms: 3188 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 8 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 8 " occ=0.50 residue: pdb=" N ALYS B 86 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 86 " occ=0.50 residue: pdb=" N AHIS C 334 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 334 " occ=0.50 Time building chain proxies: 9.43, per 1000 atoms: 0.99 Number of scatterers: 9564 At special positions: 0 Unit cell: (82.984, 102.212, 116.38, 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 48 16.00 O 1656 8.00 N 1551 7.00 C 6309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 3.4 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.541A pdb=" N TYR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 36 Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.907A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 81 through 110 removed outlier: 3.813A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 152 through 172 removed outlier: 3.787A pdb=" N VAL A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 222 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 226 through 255 removed outlier: 3.529A pdb=" N ALA A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.615A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.109A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.627A pdb=" N GLY A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.507A pdb=" N GLY A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 420 removed outlier: 3.813A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'B' and resid 13 through 35 Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.740A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.761A pdb=" N ILE B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 109 removed outlier: 4.056A pdb=" N ALYS B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.528A pdb=" N THR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 152 through 171 removed outlier: 3.762A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 222 removed outlier: 3.739A pdb=" N GLN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.837A pdb=" N PHE B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 removed outlier: 3.702A pdb=" N VAL B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.672A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 removed outlier: 3.891A pdb=" N GLU B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.842A pdb=" N VAL B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 360 through 373 removed outlier: 3.530A pdb=" N SER B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 3.712A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 402 removed outlier: 4.290A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 420 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 16 through 34 Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 76 removed outlier: 3.938A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix Processing helix chain 'C' and resid 81 through 108 removed outlier: 3.882A pdb=" N VAL C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 175 through 223 Proline residue: C 208 - end of helix removed outlier: 4.156A pdb=" N GLN C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 236 through 255 removed outlier: 4.593A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 278 removed outlier: 5.742A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 removed outlier: 3.649A pdb=" N GLU C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 313 removed outlier: 5.347A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.937A pdb=" N THR C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 4.229A pdb=" N GLN C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.550A pdb=" N VAL C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.590A pdb=" N ALA C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.771A pdb=" N ALA C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 removed outlier: 3.594A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 420 removed outlier: 4.504A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N MET C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.537A pdb=" N LYS C 427 " --> pdb=" O ASP C 424 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2086 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: 2.79 Time building geometry restraints manager: 4.07 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: 2975 1.34 - 1.46: 1451 1.46 - 1.57: 5223 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9745 Sorted by residual: bond pdb=" CG LEU C 68 " pdb=" CD1 LEU C 68 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" C ILE A 75 " pdb=" N SER A 76 " ideal model delta sigma weight residual 1.332 1.313 0.018 1.21e-02 6.83e+03 2.32e+00 bond pdb=" CB THR C 168 " pdb=" CG2 THR C 168 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" CB TRP A 20 " pdb=" CG TRP A 20 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.82e+00 bond pdb=" CB VAL A 200 " pdb=" CG2 VAL A 200 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 ... (remaining 9740 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.10: 247 106.10 - 113.07: 5592 113.07 - 120.04: 3602 120.04 - 127.01: 3748 127.01 - 133.99: 79 Bond angle restraints: 13268 Sorted by residual: angle pdb=" N GLY C 235 " pdb=" CA GLY C 235 " pdb=" C GLY C 235 " ideal model delta sigma weight residual 114.69 109.10 5.59 1.19e+00 7.06e-01 2.21e+01 angle pdb=" C VAL A 246 " pdb=" N ILE A 247 " pdb=" CA ILE A 247 " ideal model delta sigma weight residual 122.97 119.16 3.81 9.80e-01 1.04e+00 1.51e+01 angle pdb=" N ILE B 301 " pdb=" CA ILE B 301 " pdb=" C ILE B 301 " ideal model delta sigma weight residual 111.48 108.67 2.81 9.40e-01 1.13e+00 8.92e+00 angle pdb=" N THR B 378 " pdb=" CA THR B 378 " pdb=" C THR B 378 " ideal model delta sigma weight residual 109.81 116.29 -6.48 2.21e+00 2.05e-01 8.61e+00 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 109.81 116.17 -6.36 2.21e+00 2.05e-01 8.27e+00 ... (remaining 13263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5287 18.00 - 36.00: 400 36.00 - 53.99: 48 53.99 - 71.99: 6 71.99 - 89.99: 6 Dihedral angle restraints: 5747 sinusoidal: 2132 harmonic: 3615 Sorted by residual: dihedral pdb=" CA LEU B 342 " pdb=" C LEU B 342 " pdb=" N VAL B 343 " pdb=" CA VAL B 343 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU C 59 " pdb=" C LEU C 59 " pdb=" N VAL C 60 " pdb=" CA VAL C 60 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN C 110 " pdb=" C ASN C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 814 0.031 - 0.062: 585 0.062 - 0.094: 177 0.094 - 0.125: 61 0.125 - 0.156: 13 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA THR B 378 " pdb=" N THR B 378 " pdb=" C THR B 378 " pdb=" CB THR B 378 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB VAL B 105 " pdb=" CA VAL B 105 " pdb=" CG1 VAL B 105 " pdb=" CG2 VAL B 105 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA PRO B 47 " pdb=" N PRO B 47 " pdb=" C PRO B 47 " pdb=" CB PRO B 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1647 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 64 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C VAL A 64 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 64 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 65 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 245 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ILE A 245 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 245 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 246 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 381 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 382 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " 0.027 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 167 2.68 - 3.23: 10503 3.23 - 3.79: 15341 3.79 - 4.34: 20170 4.34 - 4.90: 33962 Nonbonded interactions: 80143 Sorted by model distance: nonbonded pdb=" OG1 THR C 305 " pdb=" OG1 THR C 413 " model vdw 2.122 2.440 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 287 " model vdw 2.183 2.440 nonbonded pdb=" OH TYR A 249 " pdb=" OD2 ASP A 315 " model vdw 2.197 2.440 nonbonded pdb=" O THR A 378 " pdb=" OG SER A 381 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR C 249 " pdb=" OD2 ASP C 315 " model vdw 2.224 2.440 ... (remaining 80138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) selection = (chain 'B' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) selection = (chain 'C' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 33.600 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.008 0.055 9745 Z= 0.539 Angle : 0.754 7.950 13268 Z= 0.406 Chirality : 0.046 0.156 1650 Planarity : 0.005 0.049 1632 Dihedral : 12.807 89.991 3455 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.21), residues: 1281 helix: -1.38 (0.15), residues: 997 sheet: None (None), residues: 0 loop : -2.70 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 20 HIS 0.002 0.001 HIS C 34 PHE 0.020 0.002 PHE A 302 TYR 0.016 0.002 TYR A 320 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2201 time to fit residues: 40.6130 Evaluate side-chains 94 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9745 Z= 0.193 Angle : 0.596 7.905 13268 Z= 0.299 Chirality : 0.040 0.163 1650 Planarity : 0.005 0.052 1632 Dihedral : 4.312 21.742 1369 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.70 % Allowed : 9.85 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1281 helix: -0.12 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 20 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.001 PHE A 302 TYR 0.012 0.001 TYR B 320 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 122 average time/residue: 0.2059 time to fit residues: 36.6895 Evaluate side-chains 111 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2679 time to fit residues: 2.1020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9745 Z= 0.212 Angle : 0.587 7.705 13268 Z= 0.295 Chirality : 0.040 0.179 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.118 23.783 1369 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.50 % Allowed : 13.23 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1281 helix: 0.44 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -1.68 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 16 HIS 0.002 0.001 HIS B 334 PHE 0.019 0.001 PHE A 302 TYR 0.014 0.001 TYR A 320 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.086 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 115 average time/residue: 0.1828 time to fit residues: 31.9804 Evaluate side-chains 103 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0848 time to fit residues: 1.8337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 138 ASN B 321 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9745 Z= 0.185 Angle : 0.572 7.764 13268 Z= 0.285 Chirality : 0.040 0.168 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.032 25.854 1369 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.50 % Allowed : 14.83 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1281 helix: 0.82 (0.17), residues: 1034 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 20 HIS 0.003 0.001 HIS B 334 PHE 0.017 0.001 PHE A 302 TYR 0.014 0.001 TYR B 320 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 114 average time/residue: 0.1761 time to fit residues: 31.0592 Evaluate side-chains 104 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1130 time to fit residues: 2.0074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9745 Z= 0.195 Angle : 0.586 8.101 13268 Z= 0.291 Chirality : 0.040 0.152 1650 Planarity : 0.004 0.052 1632 Dihedral : 3.999 27.417 1369 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.50 % Allowed : 16.62 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1281 helix: 0.93 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -1.34 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 16 HIS 0.003 0.001 HIS B 334 PHE 0.017 0.001 PHE A 302 TYR 0.020 0.001 TYR A 320 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.181 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 106 average time/residue: 0.1796 time to fit residues: 29.7954 Evaluate side-chains 98 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1117 time to fit residues: 1.9677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.0670 chunk 117 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9745 Z= 0.183 Angle : 0.587 7.659 13268 Z= 0.290 Chirality : 0.040 0.194 1650 Planarity : 0.004 0.051 1632 Dihedral : 3.960 27.200 1369 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.30 % Allowed : 16.92 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1281 helix: 1.06 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.16 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 16 HIS 0.003 0.001 HIS B 334 PHE 0.021 0.001 PHE B 242 TYR 0.015 0.001 TYR A 320 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.001 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.1903 time to fit residues: 31.5824 Evaluate side-chains 100 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9745 Z= 0.177 Angle : 0.613 13.110 13268 Z= 0.296 Chirality : 0.041 0.358 1650 Planarity : 0.004 0.050 1632 Dihedral : 3.942 27.216 1369 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.20 % Allowed : 17.41 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1281 helix: 1.14 (0.17), residues: 1031 sheet: None (None), residues: 0 loop : -1.09 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 16 HIS 0.003 0.001 HIS B 334 PHE 0.015 0.001 PHE A 302 TYR 0.015 0.001 TYR A 320 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.996 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.1799 time to fit residues: 29.3667 Evaluate side-chains 102 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0908 time to fit residues: 1.6186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.0040 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9745 Z= 0.179 Angle : 0.607 12.141 13268 Z= 0.293 Chirality : 0.041 0.363 1650 Planarity : 0.004 0.050 1632 Dihedral : 3.909 26.627 1369 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.40 % Allowed : 17.71 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1281 helix: 1.22 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 428 HIS 0.003 0.001 HIS B 334 PHE 0.020 0.001 PHE B 242 TYR 0.021 0.001 TYR A 320 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.109 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 114 average time/residue: 0.1832 time to fit residues: 33.0661 Evaluate side-chains 110 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1446 time to fit residues: 2.4662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.5306 > 50: distance: 44 - 68: 5.859 distance: 63 - 68: 8.907 distance: 64 - 90: 5.440 distance: 68 - 69: 6.488 distance: 69 - 70: 6.132 distance: 69 - 72: 9.144 distance: 70 - 71: 7.300 distance: 70 - 75: 10.501 distance: 71 - 101: 12.985 distance: 72 - 73: 9.592 distance: 72 - 74: 11.115 distance: 75 - 76: 9.358 distance: 76 - 77: 5.939 distance: 76 - 79: 9.356 distance: 77 - 78: 15.718 distance: 77 - 82: 12.548 distance: 79 - 80: 12.481 distance: 79 - 81: 19.899 distance: 82 - 83: 17.650 distance: 83 - 84: 9.204 distance: 83 - 86: 12.133 distance: 84 - 85: 8.739 distance: 85 - 113: 10.264 distance: 86 - 87: 15.870 distance: 87 - 88: 15.250 distance: 87 - 89: 11.714 distance: 90 - 91: 6.872 distance: 91 - 92: 10.413 distance: 91 - 94: 4.302 distance: 92 - 93: 17.791 distance: 92 - 101: 9.724 distance: 93 - 121: 26.370 distance: 95 - 96: 3.494 distance: 95 - 97: 5.696 distance: 96 - 98: 8.620 distance: 97 - 99: 4.245 distance: 98 - 100: 10.093 distance: 99 - 100: 6.760 distance: 101 - 102: 6.131 distance: 102 - 103: 5.723 distance: 102 - 105: 10.613 distance: 103 - 104: 10.982 distance: 103 - 108: 19.735 distance: 104 - 126: 17.854 distance: 105 - 106: 14.528 distance: 105 - 107: 16.387 distance: 108 - 109: 10.179 distance: 109 - 110: 5.585 distance: 109 - 112: 9.917 distance: 110 - 111: 12.839 distance: 110 - 113: 3.237 distance: 111 - 134: 34.172 distance: 113 - 114: 10.597 distance: 114 - 115: 8.378 distance: 114 - 117: 10.124 distance: 115 - 116: 26.477 distance: 115 - 121: 16.628 distance: 117 - 118: 13.899 distance: 118 - 119: 16.771 distance: 118 - 120: 27.137 distance: 121 - 122: 5.677 distance: 122 - 123: 13.904 distance: 122 - 125: 12.536 distance: 123 - 124: 8.632 distance: 123 - 126: 10.950 distance: 126 - 127: 20.046 distance: 127 - 128: 14.966 distance: 127 - 130: 10.662 distance: 128 - 129: 36.348 distance: 128 - 134: 21.880 distance: 130 - 131: 7.082 distance: 130 - 132: 18.591 distance: 131 - 133: 15.578 distance: 134 - 135: 23.337 distance: 135 - 136: 22.379 distance: 136 - 137: 18.086 distance: 136 - 138: 9.854 distance: 136 - 147: 9.857