Starting phenix.real_space_refine on Fri Jul 3 01:27:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zwm_74912/07_2026/9zwm_74912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zwm_74912/07_2026/9zwm_74912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zwm_74912/07_2026/9zwm_74912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zwm_74912/07_2026/9zwm_74912.map" model { file = "/net/cci-nas-00/data/ceres_data/9zwm_74912/07_2026/9zwm_74912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zwm_74912/07_2026/9zwm_74912.cif" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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: 7 Type Number sf(0) Gaussians K 3 8.98 5 P 3 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 7067 2.51 5 N 1832 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11067 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 5064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5064 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 26, 'TRANS': 654} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1417 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 13, 'TRANS': 174} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, '9Y0': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 2.49, per 1000 atoms: 0.22 Number of scatterers: 11067 At special positions: 0 Unit cell: (141.36, 79.05, 129.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 3 19.00 S 61 16.00 P 3 15.00 Mg 1 11.99 O 2100 8.00 N 1832 7.00 C 7067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 301.9 milliseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 64.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix removed outlier: 3.502A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.561A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.603A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.566A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.917A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.557A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.615A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.012A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.490A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.239A pdb=" N VAL A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.628A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 398 removed outlier: 3.777A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.731A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.746A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.684A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 removed outlier: 4.044A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 4.033A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix removed outlier: 3.538A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 55 removed outlier: 3.542A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.580A pdb=" N SER B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.793A pdb=" N MET B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.713A pdb=" N GLU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.701A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 5.214A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.701A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.657A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 457 through 464 removed outlier: 3.543A pdb=" N LYS B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.627A pdb=" N LYS B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 507 " --> pdb=" O ILE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.897A pdb=" N GLN B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.644A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.512A pdb=" N LYS B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.534A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.475A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 657 through 679 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 4 through 21 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.850A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.509A pdb=" N VAL C 121 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.747A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.584A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 106 Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.574A pdb=" N ILE B 147 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 5.746A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 302 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA B 514 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 304 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR B 516 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP B 302 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 319 through 324 removed outlier: 3.933A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.782A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.688A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1881 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: 1.31 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2019 1.33 - 1.45: 2565 1.45 - 1.57: 6447 1.57 - 1.69: 4 1.69 - 1.82: 111 Bond restraints: 11146 Sorted by residual: bond pdb=" C PHD B 307 " pdb=" O PHD B 307 " ideal model delta sigma weight residual 1.231 1.269 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.782 0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" CA PHD B 307 " pdb=" C PHD B 307 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 2.87e+00 bond pdb=" CG PHD B 307 " pdb=" OD2 PHD B 307 " ideal model delta sigma weight residual 1.218 1.249 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C GLY A 233 " pdb=" O GLY A 233 " ideal model delta sigma weight residual 1.243 1.234 0.009 9.30e-03 1.16e+04 9.50e-01 ... (remaining 11141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 14971 1.75 - 3.49: 127 3.49 - 5.24: 40 5.24 - 6.99: 4 6.99 - 8.74: 4 Bond angle restraints: 15146 Sorted by residual: angle pdb=" N GLY A 473 " pdb=" CA GLY A 473 " pdb=" C GLY A 473 " ideal model delta sigma weight residual 114.66 110.41 4.25 1.24e+00 6.50e-01 1.17e+01 angle pdb=" C VAL A 372 " pdb=" N PHE A 373 " pdb=" CA PHE A 373 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CG PHD B 307 " pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 125.58 116.84 8.74 3.00e+00 1.11e-01 8.48e+00 angle pdb=" OD1 PHD B 307 " pdb=" CG PHD B 307 " pdb=" OD2 PHD B 307 " ideal model delta sigma weight residual 126.03 117.66 8.37 3.00e+00 1.11e-01 7.79e+00 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 118.84 -4.94 1.80e+00 3.09e-01 7.52e+00 ... (remaining 15141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5852 17.75 - 35.50: 574 35.50 - 53.25: 167 53.25 - 71.00: 50 71.00 - 88.75: 14 Dihedral angle restraints: 6657 sinusoidal: 2536 harmonic: 4121 Sorted by residual: dihedral pdb=" CB CYS B 142 " pdb=" SG CYS B 142 " pdb=" SG CYS B 191 " pdb=" CB CYS B 191 " ideal model delta sinusoidal sigma weight residual 93.00 56.97 36.03 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA LEU B 314 " pdb=" C LEU B 314 " pdb=" N GLY B 315 " pdb=" CA GLY B 315 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN C 131 " pdb=" C ASN C 131 " pdb=" N ILE C 132 " pdb=" CA ILE C 132 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1157 0.028 - 0.056: 423 0.056 - 0.084: 139 0.084 - 0.111: 78 0.111 - 0.139: 18 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE A 34 " pdb=" N ILE A 34 " pdb=" C ILE A 34 " pdb=" CB ILE A 34 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE B 323 " pdb=" N ILE B 323 " pdb=" C ILE B 323 " pdb=" CB ILE B 323 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1812 not shown) Planarity restraints: 1915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 10 " 0.029 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 11 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 11 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 11 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 4 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.12e+00 pdb=" C LYS B 4 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS B 4 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN B 5 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 116 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 117 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " 0.018 5.00e-02 4.00e+02 ... (remaining 1912 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3627 2.83 - 3.41: 12477 3.41 - 3.99: 22794 3.99 - 4.56: 31705 4.56 - 5.14: 44130 Nonbonded interactions: 114733 Sorted by model distance: nonbonded pdb=" O HOH A 711 " pdb=" O HOH A 765 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU A 413 " pdb=" OG SER A 506 " model vdw 2.257 3.040 nonbonded pdb=" O PHE A 471 " pdb=" O HOH A 701 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP C 95 " pdb=" O HOH C 301 " model vdw 2.267 3.040 nonbonded pdb=" O HOH A 724 " pdb=" O HOH A 740 " model vdw 2.268 3.040 ... (remaining 114728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 : 0.002 0.038 11147 Z= 0.102 Angle : 0.500 8.737 15148 Z= 0.253 Chirality : 0.037 0.139 1815 Planarity : 0.003 0.045 1915 Dihedral : 16.765 88.754 4006 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.14 % Allowed : 18.26 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1444 helix: 1.12 (0.18), residues: 841 sheet: -1.63 (0.55), residues: 84 loop : -0.23 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.022 0.002 TYR B 641 PHE 0.013 0.001 PHE B 623 TRP 0.015 0.001 TRP A 176 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (11146) covalent geometry : angle 0.49977 / 0.25 (15146) SS BOND : bond 0.00222 / 0.12 ( 1) SS BOND : angle 0.74944 / 0.41 ( 2) hydrogen bonds : bond 0.22144 / 14.47 ( 650) hydrogen bonds : angle 6.85462 / 5.20 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.342 Fit side-chains REVERT: B 206 MET cc_start: 0.6688 (ttm) cc_final: 0.6158 (tpp) outliers start: 13 outliers final: 10 residues processed: 136 average time/residue: 0.5840 time to fit residues: 85.4446 Evaluate side-chains 131 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.0570 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 477 ASN B 16 GLN B 563 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094098 restraints weight = 10582.420| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.58 r_work: 0.2942 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11147 Z= 0.120 Angle : 0.514 6.421 15148 Z= 0.270 Chirality : 0.040 0.165 1815 Planarity : 0.004 0.042 1915 Dihedral : 8.847 88.356 1626 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.93 % Allowed : 17.30 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.22), residues: 1444 helix: 1.67 (0.17), residues: 852 sheet: -1.66 (0.54), residues: 86 loop : -0.42 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.020 0.001 TYR A 381 PHE 0.014 0.001 PHE B 578 TRP 0.012 0.001 TRP A 176 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (11146) covalent geometry : angle 0.51348 / 0.27 (15146) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 0.79881 / 0.43 ( 2) hydrogen bonds : bond 0.05165 / 3.44 ( 650) hydrogen bonds : angle 4.63300 / 3.54 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: B 206 MET cc_start: 0.6756 (ttm) cc_final: 0.6447 (ttm) outliers start: 22 outliers final: 6 residues processed: 138 average time/residue: 0.5883 time to fit residues: 87.5749 Evaluate side-chains 123 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 302 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN B 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.171579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.091972 restraints weight = 10614.584| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.58 r_work: 0.2908 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11147 Z= 0.126 Angle : 0.504 6.656 15148 Z= 0.263 Chirality : 0.040 0.159 1815 Planarity : 0.004 0.046 1915 Dihedral : 8.426 87.824 1615 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.84 % Allowed : 17.73 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1444 helix: 1.74 (0.17), residues: 849 sheet: -1.54 (0.59), residues: 72 loop : -0.51 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 438 TYR 0.023 0.002 TYR A 381 PHE 0.013 0.001 PHE B 578 TRP 0.015 0.001 TRP A 176 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11146) covalent geometry : angle 0.50409 / 0.26 (15146) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 0.84532 / 0.46 ( 2) hydrogen bonds : bond 0.05088 / 3.39 ( 650) hydrogen bonds : angle 4.42163 / 3.37 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 107 ARG cc_start: 0.4011 (mmm-85) cc_final: 0.3039 (mmp80) REVERT: B 312 ILE cc_start: 0.3794 (OUTLIER) cc_final: 0.3266 (mt) REVERT: B 388 ILE cc_start: 0.0420 (OUTLIER) cc_final: 0.0172 (mm) REVERT: C 96 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8150 (mtpp) outliers start: 21 outliers final: 11 residues processed: 135 average time/residue: 0.6166 time to fit residues: 89.7181 Evaluate side-chains 126 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 94 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 88 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 205 ASN A 477 ASN B 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094024 restraints weight = 10664.700| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.53 r_work: 0.2949 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11147 Z= 0.117 Angle : 0.489 6.607 15148 Z= 0.255 Chirality : 0.039 0.163 1815 Planarity : 0.004 0.047 1915 Dihedral : 8.174 86.489 1614 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.02 % Allowed : 18.09 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.22), residues: 1444 helix: 1.80 (0.17), residues: 850 sheet: -1.69 (0.53), residues: 84 loop : -0.46 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 394 TYR 0.023 0.002 TYR A 381 PHE 0.012 0.001 PHE B 578 TRP 0.014 0.001 TRP A 176 HIS 0.002 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (11146) covalent geometry : angle 0.48880 / 0.25 (15146) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.86216 / 0.47 ( 2) hydrogen bonds : bond 0.04658 / 3.10 ( 650) hydrogen bonds : angle 4.29557 / 3.27 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.282 Fit side-chains REVERT: A 410 ASP cc_start: 0.8229 (m-30) cc_final: 0.7875 (m-30) REVERT: B 107 ARG cc_start: 0.3902 (mmm-85) cc_final: 0.3123 (mmp80) REVERT: B 198 THR cc_start: 0.4425 (OUTLIER) cc_final: 0.4195 (m) REVERT: B 202 ARG cc_start: 0.7533 (mtt90) cc_final: 0.7267 (mtt90) REVERT: B 312 ILE cc_start: 0.3936 (OUTLIER) cc_final: 0.3366 (mt) REVERT: C 96 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8220 (mtpp) outliers start: 23 outliers final: 9 residues processed: 136 average time/residue: 0.6109 time to fit residues: 89.7151 Evaluate side-chains 125 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 125 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 26 optimal weight: 0.0050 chunk 19 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 477 ASN B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.172575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093675 restraints weight = 10655.271| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.58 r_work: 0.2932 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11147 Z= 0.110 Angle : 0.477 6.571 15148 Z= 0.248 Chirality : 0.039 0.166 1815 Planarity : 0.004 0.048 1915 Dihedral : 8.002 85.353 1614 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.76 % Allowed : 18.70 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1444 helix: 1.92 (0.18), residues: 846 sheet: -1.77 (0.52), residues: 88 loop : -0.49 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.023 0.002 TYR A 381 PHE 0.012 0.001 PHE B 578 TRP 0.015 0.001 TRP A 176 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (11146) covalent geometry : angle 0.47684 / 0.25 (15146) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 0.85925 / 0.46 ( 2) hydrogen bonds : bond 0.04427 / 2.95 ( 650) hydrogen bonds : angle 4.21509 / 3.21 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.427 Fit side-chains REVERT: A 410 ASP cc_start: 0.8216 (m-30) cc_final: 0.7860 (m-30) REVERT: B 63 LEU cc_start: 0.8669 (tp) cc_final: 0.8334 (mm) REVERT: B 107 ARG cc_start: 0.3874 (mmm-85) cc_final: 0.2987 (mmp80) REVERT: B 312 ILE cc_start: 0.3844 (OUTLIER) cc_final: 0.3267 (mt) REVERT: B 388 ILE cc_start: 0.0364 (OUTLIER) cc_final: 0.0112 (mm) REVERT: C 96 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8100 (mtpp) REVERT: D 13 PHE cc_start: 0.7902 (m-80) cc_final: 0.7565 (m-10) outliers start: 20 outliers final: 7 residues processed: 137 average time/residue: 0.6367 time to fit residues: 94.1431 Evaluate side-chains 126 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 96 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 16 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 477 ASN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.092245 restraints weight = 10644.121| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.55 r_work: 0.2911 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11147 Z= 0.123 Angle : 0.497 6.675 15148 Z= 0.260 Chirality : 0.040 0.179 1815 Planarity : 0.004 0.049 1915 Dihedral : 8.065 85.995 1614 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.58 % Allowed : 18.70 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.22), residues: 1444 helix: 1.85 (0.17), residues: 849 sheet: -1.64 (0.54), residues: 84 loop : -0.52 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 394 TYR 0.024 0.002 TYR A 381 PHE 0.012 0.001 PHE B 578 TRP 0.016 0.001 TRP A 176 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11146) covalent geometry : angle 0.49656 / 0.26 (15146) SS BOND : bond 0.00079 / 0.04 ( 1) SS BOND : angle 0.84160 / 0.45 ( 2) hydrogen bonds : bond 0.04699 / 3.13 ( 650) hydrogen bonds : angle 4.25517 / 3.24 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.508 Fit side-chains REVERT: A 410 ASP cc_start: 0.8253 (m-30) cc_final: 0.7895 (m-30) REVERT: B 107 ARG cc_start: 0.4006 (mmm-85) cc_final: 0.3097 (mmp80) REVERT: B 312 ILE cc_start: 0.3832 (OUTLIER) cc_final: 0.3232 (mt) REVERT: C 96 LYS cc_start: 0.8356 (ttmm) cc_final: 0.8118 (mtpp) REVERT: D 13 PHE cc_start: 0.7914 (m-80) cc_final: 0.7572 (m-10) outliers start: 18 outliers final: 9 residues processed: 135 average time/residue: 0.6446 time to fit residues: 93.6678 Evaluate side-chains 127 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 477 ASN B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.089000 restraints weight = 10526.330| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.58 r_work: 0.2866 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11147 Z= 0.176 Angle : 0.556 7.029 15148 Z= 0.291 Chirality : 0.043 0.194 1815 Planarity : 0.004 0.049 1915 Dihedral : 8.455 88.668 1614 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.11 % Allowed : 18.00 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1444 helix: 1.62 (0.17), residues: 849 sheet: -1.52 (0.59), residues: 72 loop : -0.59 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 32 TYR 0.024 0.002 TYR A 381 PHE 0.017 0.002 PHE A 527 TRP 0.017 0.001 TRP A 176 HIS 0.004 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (11146) covalent geometry : angle 0.55564 / 0.29 (15146) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 0.73860 / 0.39 ( 2) hydrogen bonds : bond 0.05506 / 3.66 ( 650) hydrogen bonds : angle 4.45404 / 3.40 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.403 Fit side-chains REVERT: A 410 ASP cc_start: 0.8250 (m-30) cc_final: 0.7922 (m-30) REVERT: B 107 ARG cc_start: 0.3940 (mmm-85) cc_final: 0.3013 (mmp80) REVERT: B 388 ILE cc_start: 0.0383 (OUTLIER) cc_final: 0.0124 (mm) REVERT: C 96 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8112 (mtpp) outliers start: 24 outliers final: 13 residues processed: 136 average time/residue: 0.6508 time to fit residues: 95.4668 Evaluate side-chains 130 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 135 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 211 GLN A 477 ASN B 563 HIS C 165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.091313 restraints weight = 10572.555| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.58 r_work: 0.2902 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11147 Z= 0.126 Angle : 0.507 6.850 15148 Z= 0.264 Chirality : 0.040 0.192 1815 Planarity : 0.004 0.049 1915 Dihedral : 8.253 87.175 1614 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.76 % Allowed : 18.26 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1444 helix: 1.82 (0.17), residues: 844 sheet: -1.54 (0.52), residues: 89 loop : -0.57 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.023 0.002 TYR A 381 PHE 0.011 0.001 PHE B 578 TRP 0.018 0.001 TRP A 176 HIS 0.003 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (11146) covalent geometry : angle 0.50674 / 0.26 (15146) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.72058 / 0.38 ( 2) hydrogen bonds : bond 0.04717 / 3.14 ( 650) hydrogen bonds : angle 4.29098 / 3.27 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.421 Fit side-chains REVERT: A 410 ASP cc_start: 0.8231 (m-30) cc_final: 0.7891 (m-30) REVERT: B 107 ARG cc_start: 0.3873 (mmm-85) cc_final: 0.2979 (mmp80) REVERT: B 544 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6941 (mm-30) REVERT: C 96 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (mtpp) outliers start: 20 outliers final: 15 residues processed: 130 average time/residue: 0.5738 time to fit residues: 80.2810 Evaluate side-chains 130 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 123 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 211 GLN A 477 ASN B 563 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.090412 restraints weight = 10431.747| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.57 r_work: 0.2888 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11147 Z= 0.140 Angle : 0.524 7.126 15148 Z= 0.273 Chirality : 0.041 0.201 1815 Planarity : 0.004 0.049 1915 Dihedral : 8.329 88.527 1614 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.84 % Allowed : 18.26 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1444 helix: 1.77 (0.17), residues: 842 sheet: -1.55 (0.53), residues: 89 loop : -0.58 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.024 0.002 TYR A 381 PHE 0.013 0.001 PHE A 527 TRP 0.018 0.001 TRP A 176 HIS 0.003 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11146) covalent geometry : angle 0.52424 / 0.27 (15146) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 0.66003 / 0.35 ( 2) hydrogen bonds : bond 0.05004 / 3.33 ( 650) hydrogen bonds : angle 4.34060 / 3.31 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 410 ASP cc_start: 0.8240 (m-30) cc_final: 0.7906 (m-30) REVERT: B 107 ARG cc_start: 0.4008 (mmm-85) cc_final: 0.3050 (mmp80) REVERT: B 206 MET cc_start: 0.6838 (ttm) cc_final: 0.6581 (ttm) REVERT: C 96 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8155 (mtpp) outliers start: 21 outliers final: 16 residues processed: 134 average time/residue: 0.5674 time to fit residues: 82.0921 Evaluate side-chains 133 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1764 > 50: distance: 50 - 72: 23.315 distance: 65 - 72: 20.082 distance: 72 - 73: 23.537 distance: 73 - 74: 30.654 distance: 73 - 76: 30.399 distance: 74 - 75: 34.349 distance: 74 - 84: 41.833 distance: 76 - 77: 15.960 distance: 77 - 78: 17.743 distance: 77 - 79: 13.359 distance: 78 - 80: 9.396 distance: 79 - 81: 10.618 distance: 80 - 82: 13.949 distance: 81 - 82: 20.775 distance: 82 - 83: 4.344 distance: 84 - 85: 22.939 distance: 85 - 86: 31.035 distance: 85 - 88: 10.276 distance: 86 - 87: 35.632 distance: 86 - 90: 48.324 distance: 88 - 89: 36.130 distance: 90 - 91: 8.670 distance: 90 - 177: 27.814 distance: 91 - 92: 44.048 distance: 91 - 94: 30.965 distance: 92 - 93: 47.279 distance: 92 - 99: 8.338 distance: 93 - 174: 31.958 distance: 94 - 95: 26.774 distance: 95 - 96: 33.386 distance: 96 - 97: 30.157 distance: 96 - 98: 19.790 distance: 99 - 100: 8.475 distance: 100 - 101: 23.372 distance: 100 - 103: 55.062 distance: 101 - 102: 28.600 distance: 101 - 108: 9.823 distance: 103 - 104: 17.866 distance: 104 - 105: 27.206 distance: 105 - 106: 13.295 distance: 105 - 107: 13.682 distance: 108 - 109: 22.047 distance: 108 - 114: 34.068 distance: 109 - 110: 29.203 distance: 109 - 112: 18.775 distance: 110 - 111: 12.219 distance: 110 - 115: 44.986 distance: 112 - 113: 25.072 distance: 113 - 114: 43.453 distance: 115 - 116: 17.948 distance: 116 - 117: 23.959 distance: 116 - 119: 40.568 distance: 117 - 118: 21.277 distance: 117 - 123: 18.137 distance: 119 - 120: 35.677 distance: 120 - 121: 20.649 distance: 120 - 122: 13.487 distance: 123 - 124: 13.717 distance: 124 - 125: 14.088 distance: 124 - 127: 31.160 distance: 125 - 126: 26.143 distance: 125 - 130: 56.886 distance: 127 - 128: 24.727 distance: 127 - 129: 21.058 distance: 130 - 131: 31.754 distance: 131 - 132: 21.218 distance: 131 - 134: 35.264 distance: 132 - 133: 7.359 distance: 132 - 139: 46.267 distance: 134 - 135: 43.613 distance: 135 - 136: 38.523 distance: 136 - 137: 33.969 distance: 137 - 138: 15.392 distance: 139 - 140: 23.226 distance: 140 - 141: 14.255 distance: 140 - 143: 12.099 distance: 141 - 142: 23.639 distance: 141 - 151: 11.539 distance: 143 - 144: 9.101 distance: 144 - 145: 22.396 distance: 144 - 146: 10.104 distance: 145 - 147: 13.303 distance: 146 - 148: 17.141 distance: 147 - 149: 6.682 distance: 148 - 149: 14.401 distance: 149 - 150: 7.526 distance: 151 - 152: 15.164 distance: 152 - 155: 5.233 distance: 153 - 154: 8.800 distance: 153 - 159: 5.002 distance: 155 - 156: 17.552 distance: 155 - 157: 7.846 distance: 156 - 158: 25.993