Starting phenix.real_space_refine on Wed Feb 12 05:42:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p9v_13267/02_2025/7p9v_13267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p9v_13267/02_2025/7p9v_13267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p9v_13267/02_2025/7p9v_13267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p9v_13267/02_2025/7p9v_13267.map" model { file = "/net/cci-nas-00/data/ceres_data/7p9v_13267/02_2025/7p9v_13267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p9v_13267/02_2025/7p9v_13267.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.046 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 27 5.16 5 C 4751 2.51 5 N 1185 2.21 5 O 1323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7286 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3616 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain: "B" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3558 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 23, 'TRANS': 431} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.99, per 1000 atoms: 0.68 Number of scatterers: 7286 At special positions: 0 Unit cell: (85.696, 79.872, 131.456, 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 27 16.00 O 1323 8.00 N 1185 7.00 C 4751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 158 " distance=2.21 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 932.0 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 57.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 179 through 208 removed outlier: 3.574A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.704A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.336A pdb=" N LYS A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.746A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 414 through 427 removed outlier: 4.261A pdb=" N VAL A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.650A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.811A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.624A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 4.006A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.809A pdb=" N THR B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 Proline residue: B 66 - end of helix removed outlier: 3.602A pdb=" N ASN B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 105 removed outlier: 3.653A pdb=" N ILE B 82 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.899A pdb=" N GLU B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.618A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 removed outlier: 3.579A pdb=" N ALA B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.536A pdb=" N ILE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 211 removed outlier: 3.927A pdb=" N ILE B 190 " --> pdb=" O TRP B 186 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 234 through 246 removed outlier: 3.739A pdb=" N ALA B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 292 removed outlier: 4.365A pdb=" N ILE B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 302 through 312 removed outlier: 3.772A pdb=" N THR B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.589A pdb=" N ALA B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Proline residue: B 320 - end of helix removed outlier: 4.944A pdb=" N ALA B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 348 removed outlier: 3.985A pdb=" N LEU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.536A pdb=" N VAL B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 371 through 382 removed outlier: 4.265A pdb=" N LEU B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 402 removed outlier: 4.271A pdb=" N ASN B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.858A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 439 removed outlier: 5.537A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 443 removed outlier: 3.786A pdb=" N LEU B 443 " --> pdb=" O ALA B 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.582A pdb=" N TYR B 464 " --> pdb=" O VAL B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 7.316A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 308 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.171A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.567A pdb=" N PHE A 545 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 611 removed outlier: 7.052A pdb=" N LEU A 624 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 359 318 hydrogen bonds defined for protein. 924 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: 1.69 Time building geometry restraints manager: 2.28 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: 2252 1.34 - 1.46: 1535 1.46 - 1.58: 3631 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 7463 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.38e+00 bond pdb=" CA LEU A 335 " pdb=" C LEU A 335 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.43e-02 4.89e+03 4.44e+00 bond pdb=" C LEU A 335 " pdb=" N GLU A 336 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 ... (remaining 7458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 9909 2.20 - 4.40: 209 4.40 - 6.59: 24 6.59 - 8.79: 6 8.79 - 10.99: 3 Bond angle restraints: 10151 Sorted by residual: angle pdb=" N ILE B 205 " pdb=" CA ILE B 205 " pdb=" C ILE B 205 " ideal model delta sigma weight residual 111.90 109.22 2.68 8.10e-01 1.52e+00 1.10e+01 angle pdb=" N GLY B 334 " pdb=" CA GLY B 334 " pdb=" C GLY B 334 " ideal model delta sigma weight residual 115.66 110.27 5.39 1.63e+00 3.76e-01 1.10e+01 angle pdb=" N LEU B 430 " pdb=" CA LEU B 430 " pdb=" C LEU B 430 " ideal model delta sigma weight residual 114.75 110.66 4.09 1.26e+00 6.30e-01 1.05e+01 angle pdb=" N VAL B 76 " pdb=" CA VAL B 76 " pdb=" C VAL B 76 " ideal model delta sigma weight residual 111.56 108.80 2.76 8.60e-01 1.35e+00 1.03e+01 angle pdb=" CA TRP B 476 " pdb=" CB TRP B 476 " pdb=" CG TRP B 476 " ideal model delta sigma weight residual 113.60 107.53 6.07 1.90e+00 2.77e-01 1.02e+01 ... (remaining 10146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 4167 21.89 - 43.78: 280 43.78 - 65.66: 29 65.66 - 87.55: 11 87.55 - 109.44: 9 Dihedral angle restraints: 4496 sinusoidal: 1857 harmonic: 2639 Sorted by residual: dihedral pdb=" CA PRO B 320 " pdb=" C PRO B 320 " pdb=" N ILE B 321 " pdb=" CA ILE B 321 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LYS A 270 " pdb=" C LYS A 270 " pdb=" N ASP A 271 " pdb=" CA ASP A 271 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ALA B 429 " pdb=" C ALA B 429 " pdb=" N LEU B 430 " pdb=" CA LEU B 430 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1125 0.092 - 0.185: 67 0.185 - 0.277: 2 0.277 - 0.369: 0 0.369 - 0.461: 1 Chirality restraints: 1195 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1192 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 476 " -0.032 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP B 476 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP B 476 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 476 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 476 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 476 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 476 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 476 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 476 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 476 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 627 " -0.060 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 628 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 321 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C ILE B 321 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 321 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE B 322 " 0.012 2.00e-02 2.50e+03 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 138 2.66 - 3.22: 7319 3.22 - 3.78: 11063 3.78 - 4.34: 15376 4.34 - 4.90: 25040 Nonbonded interactions: 58936 Sorted by model distance: nonbonded pdb=" OD2 ASP B 446 " pdb=" OG SER B 449 " model vdw 2.104 3.040 nonbonded pdb=" OH TYR B 111 " pdb=" OE2 GLU B 348 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR A 469 " pdb=" O PRO A 488 " model vdw 2.110 3.040 nonbonded pdb=" O TRP A 492 " pdb=" NZ LYS A 511 " model vdw 2.202 3.120 nonbonded pdb=" OG SER B 75 " pdb=" O ALA B 224 " model vdw 2.203 3.040 ... (remaining 58931 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.320 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.005 0.056 7463 Z= 0.332 Angle : 0.819 10.988 10151 Z= 0.439 Chirality : 0.048 0.461 1195 Planarity : 0.005 0.093 1258 Dihedral : 15.249 109.438 2797 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.67 (0.27), residues: 915 helix: -1.08 (0.24), residues: 461 sheet: -2.92 (0.63), residues: 63 loop : -2.34 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP B 476 HIS 0.011 0.001 HIS B 350 PHE 0.023 0.002 PHE A 291 TYR 0.015 0.002 TYR A 629 ARG 0.005 0.001 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: B 476 TRP cc_start: 0.3558 (m100) cc_final: 0.2302 (m100) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1856 time to fit residues: 41.0695 Evaluate side-chains 125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.0980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.155599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139501 restraints weight = 11764.766| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.15 r_work: 0.3649 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7463 Z= 0.212 Angle : 0.710 11.276 10151 Z= 0.345 Chirality : 0.045 0.328 1195 Planarity : 0.005 0.058 1258 Dihedral : 10.885 89.473 1151 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.16 % Allowed : 9.00 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.34 (0.27), residues: 915 helix: -0.60 (0.23), residues: 482 sheet: -2.57 (0.62), residues: 64 loop : -2.60 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 476 HIS 0.006 0.001 HIS B 359 PHE 0.026 0.002 PHE A 524 TYR 0.027 0.002 TYR A 313 ARG 0.005 0.001 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.895 Fit side-chains REVERT: B 476 TRP cc_start: 0.4514 (m100) cc_final: 0.3341 (m100) outliers start: 9 outliers final: 5 residues processed: 157 average time/residue: 0.1595 time to fit residues: 35.5659 Evaluate side-chains 133 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 18 optimal weight: 0.0470 chunk 33 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** 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 = 0.3938 r_free = 0.3938 target = 0.157360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141609 restraints weight = 11915.795| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.16 r_work: 0.3661 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7463 Z= 0.188 Angle : 0.665 10.120 10151 Z= 0.319 Chirality : 0.044 0.304 1195 Planarity : 0.004 0.053 1258 Dihedral : 9.592 73.308 1151 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.19 % Allowed : 12.47 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.86 (0.27), residues: 915 helix: -0.17 (0.24), residues: 475 sheet: -2.49 (0.64), residues: 64 loop : -2.39 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 476 HIS 0.005 0.001 HIS B 359 PHE 0.025 0.002 PHE A 524 TYR 0.029 0.001 TYR A 313 ARG 0.003 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.826 Fit side-chains REVERT: A 186 LEU cc_start: 0.8042 (mm) cc_final: 0.7762 (mp) REVERT: A 485 MET cc_start: 0.7197 (ppp) cc_final: 0.6168 (tpt) REVERT: A 564 PHE cc_start: 0.8315 (m-80) cc_final: 0.8094 (m-80) REVERT: B 417 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.4889 (ppp) REVERT: B 476 TRP cc_start: 0.4489 (m100) cc_final: 0.3356 (m100) REVERT: B 480 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6165 (ttm) outliers start: 17 outliers final: 9 residues processed: 155 average time/residue: 0.1510 time to fit residues: 33.5202 Evaluate side-chains 143 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 36 optimal weight: 0.0570 chunk 33 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** 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 = 0.4053 r_free = 0.4053 target = 0.163239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146914 restraints weight = 12255.582| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.36 r_work: 0.3766 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7463 Z= 0.189 Angle : 0.647 10.729 10151 Z= 0.310 Chirality : 0.043 0.288 1195 Planarity : 0.004 0.055 1258 Dihedral : 8.581 59.858 1151 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.57 % Allowed : 14.40 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.60 (0.28), residues: 915 helix: 0.06 (0.24), residues: 473 sheet: -2.17 (0.67), residues: 64 loop : -2.32 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 476 HIS 0.003 0.001 HIS B 350 PHE 0.026 0.001 PHE A 524 TYR 0.029 0.001 TYR A 313 ARG 0.004 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.784 Fit side-chains REVERT: A 485 MET cc_start: 0.6955 (ppp) cc_final: 0.6070 (tpt) REVERT: B 315 PHE cc_start: 0.7533 (p90) cc_final: 0.7313 (p90) REVERT: B 417 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5636 (ppp) REVERT: B 476 TRP cc_start: 0.4026 (m100) cc_final: 0.3015 (m100) REVERT: B 480 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.6080 (ttm) outliers start: 20 outliers final: 13 residues processed: 152 average time/residue: 0.1552 time to fit residues: 34.0477 Evaluate side-chains 148 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.156868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140913 restraints weight = 11743.128| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.15 r_work: 0.3663 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7463 Z= 0.196 Angle : 0.658 13.997 10151 Z= 0.310 Chirality : 0.043 0.283 1195 Planarity : 0.004 0.054 1258 Dihedral : 7.951 57.618 1151 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.57 % Allowed : 16.20 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.47 (0.28), residues: 915 helix: 0.15 (0.24), residues: 474 sheet: -2.00 (0.72), residues: 64 loop : -2.25 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.003 0.001 HIS B 350 PHE 0.026 0.001 PHE A 524 TYR 0.029 0.001 TYR A 313 ARG 0.004 0.000 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.765 Fit side-chains REVERT: A 485 MET cc_start: 0.7186 (ppp) cc_final: 0.6172 (tpt) REVERT: B 315 PHE cc_start: 0.7741 (p90) cc_final: 0.7506 (p90) REVERT: B 417 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5683 (ppp) REVERT: B 476 TRP cc_start: 0.4402 (m100) cc_final: 0.3146 (m100) REVERT: B 480 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6238 (ttm) outliers start: 20 outliers final: 14 residues processed: 149 average time/residue: 0.1404 time to fit residues: 31.0582 Evaluate side-chains 147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/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-dev-5592/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-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/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-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/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-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3016 > 50: distance: 66 - 71: 20.924 distance: 71 - 72: 17.941 distance: 72 - 75: 9.650 distance: 73 - 74: 5.805 distance: 75 - 76: 9.851 distance: 76 - 77: 11.316 distance: 76 - 78: 17.628 distance: 79 - 80: 4.264 distance: 80 - 81: 6.121 distance: 80 - 83: 6.796 distance: 81 - 82: 4.710 distance: 81 - 87: 4.016 distance: 83 - 84: 5.639 distance: 84 - 85: 8.998 distance: 87 - 88: 4.428 distance: 88 - 91: 4.276 distance: 89 - 90: 14.731 distance: 89 - 95: 10.914 distance: 91 - 92: 10.923 distance: 92 - 93: 5.868 distance: 92 - 94: 4.565 distance: 95 - 96: 7.277 distance: 96 - 97: 18.062 distance: 96 - 99: 21.219 distance: 97 - 98: 15.152 distance: 97 - 102: 14.433 distance: 99 - 100: 16.948 distance: 99 - 101: 24.015 distance: 102 - 103: 9.088 distance: 102 - 108: 22.207 distance: 103 - 104: 12.499 distance: 103 - 106: 24.728 distance: 104 - 105: 21.129 distance: 104 - 109: 27.337 distance: 106 - 107: 11.051 distance: 107 - 108: 23.439 distance: 109 - 110: 11.183 distance: 110 - 111: 6.725 distance: 110 - 113: 10.132 distance: 111 - 112: 16.277 distance: 111 - 117: 29.537 distance: 113 - 114: 15.579 distance: 114 - 115: 27.165 distance: 114 - 116: 20.611 distance: 117 - 118: 10.279 distance: 118 - 119: 11.513 distance: 118 - 121: 11.387 distance: 119 - 120: 15.226 distance: 119 - 129: 9.586 distance: 121 - 122: 7.942 distance: 122 - 123: 9.372 distance: 122 - 124: 10.176 distance: 123 - 125: 7.456 distance: 124 - 126: 13.025 distance: 125 - 127: 11.085 distance: 126 - 127: 11.266 distance: 127 - 128: 7.710 distance: 129 - 130: 16.364 distance: 130 - 131: 11.300 distance: 130 - 133: 19.495 distance: 131 - 132: 8.432 distance: 131 - 140: 13.012 distance: 133 - 134: 6.794 distance: 134 - 135: 4.724 distance: 135 - 136: 5.027 distance: 140 - 141: 10.314 distance: 141 - 142: 26.946 distance: 142 - 143: 30.010 distance: 142 - 144: 14.014 distance: 144 - 145: 5.005 distance: 145 - 146: 13.686 distance: 145 - 148: 11.411 distance: 146 - 147: 15.261 distance: 146 - 153: 6.874 distance: 148 - 149: 20.813 distance: 149 - 150: 14.785 distance: 150 - 151: 13.640 distance: 150 - 152: 18.320