Starting phenix.real_space_refine on Sun Apr 5 02:28:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwy_62620/04_2026/9kwy_62620.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwy_62620/04_2026/9kwy_62620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwy_62620/04_2026/9kwy_62620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwy_62620/04_2026/9kwy_62620.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwy_62620/04_2026/9kwy_62620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwy_62620/04_2026/9kwy_62620.cif" } resolution = 2.82 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= 0.002 sd= 0.028 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 32 5.16 5 C 4736 2.51 5 N 1238 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7342 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4185 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 544} Chain breaks: 2 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 591 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 36, 'ASP:plan': 17, 'GLN:plan1': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 317 Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1391 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 767 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: 1.78, per 1000 atoms: 0.24 Number of scatterers: 7342 At special positions: 0 Unit cell: (117, 100.1, 81.9, 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 32 16.00 O 1336 8.00 N 1238 7.00 C 4736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 90 " " NAG A 602 " - " ASN A 546 " " NAG D 1 " - " ASN G 343 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 309.7 milliseconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 13 sheets defined 45.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.437A pdb=" N GLU A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.671A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.665A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.883A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.904A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.563A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.851A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.201A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.548A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.578A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.987A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 386 removed outlier: 3.810A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 388 No H-bonds generated for 'chain 'A' and resid 387 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 398 through 413 removed outlier: 4.599A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.726A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.098A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.664A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.818A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'G' and resid 337 through 343 removed outlier: 3.846A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 371 removed outlier: 3.740A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 389 Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.991A pdb=" N PHE B 83 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.549A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.560A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.597A pdb=" N LYS G 356 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 6 removed outlier: 5.607A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.677A pdb=" N VAL B 13 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.677A pdb=" N VAL B 13 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.716A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.088A pdb=" N GLU C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 113 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.088A pdb=" N GLU C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 113 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL C 108 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 21 357 hydrogen bonds defined for protein. 990 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: 1.06 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2297 1.34 - 1.46: 1660 1.46 - 1.57: 3543 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7548 Sorted by residual: bond pdb=" CA THR C 53 " pdb=" C THR C 53 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.80e-02 3.09e+03 4.50e+00 bond pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.20e-02 6.94e+03 2.55e+00 bond pdb=" C2 BMA D 3 " pdb=" C3 BMA D 3 " ideal model delta sigma weight residual 1.544 1.513 0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" CA THR G 500 " pdb=" C THR G 500 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.34e-02 5.57e+03 1.66e+00 bond pdb=" CA ASP C 62 " pdb=" C ASP C 62 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.80e-02 3.09e+03 1.63e+00 ... (remaining 7543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 9900 1.51 - 3.01: 347 3.01 - 4.52: 55 4.52 - 6.03: 18 6.03 - 7.53: 4 Bond angle restraints: 10324 Sorted by residual: angle pdb=" C ASN C 61 " pdb=" N ASP C 62 " pdb=" CA ASP C 62 " ideal model delta sigma weight residual 122.31 114.78 7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 110.20 114.79 -4.59 1.32e+00 5.74e-01 1.21e+01 angle pdb=" C ASN A 508 " pdb=" N ASP A 509 " pdb=" CA ASP A 509 " ideal model delta sigma weight residual 122.40 126.93 -4.53 1.45e+00 4.76e-01 9.78e+00 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 109.81 116.49 -6.68 2.21e+00 2.05e-01 9.12e+00 angle pdb=" CA LYS A 234 " pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 118.44 122.48 -4.04 1.59e+00 3.96e-01 6.46e+00 ... (remaining 10319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 4153 21.50 - 43.00: 219 43.00 - 64.50: 19 64.50 - 86.00: 10 86.00 - 107.50: 13 Dihedral angle restraints: 4414 sinusoidal: 1554 harmonic: 2860 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -132.52 46.52 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CA THR G 500 " pdb=" C THR G 500 " pdb=" N ASN G 501 " pdb=" CA ASN G 501 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA TRP C 104 " pdb=" C TRP C 104 " pdb=" N TYR C 105 " pdb=" CA TYR C 105 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 4411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.851: 1160 0.851 - 1.702: 0 1.702 - 2.553: 0 2.553 - 3.404: 1 3.404 - 4.255: 1 Chirality restraints: 1162 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 1.85 -4.25 2.00e-02 2.50e+03 4.53e+04 chirality pdb=" C1 FUC D 4 " pdb=" O6 NAG D 1 " pdb=" C2 FUC D 4 " pdb=" O5 FUC D 4 " both_signs ideal model delta sigma weight residual False -2.40 0.75 -3.15 2.00e-02 2.50e+03 2.48e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.69e+03 ... (remaining 1159 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO G 463 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 491 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO A 492 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 492 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 492 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 400 " -0.009 2.00e-02 2.50e+03 1.18e-02 2.46e+00 pdb=" CG PHE A 400 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 400 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 400 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 400 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 400 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 400 " 0.001 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 108 2.66 - 3.22: 6947 3.22 - 3.78: 11681 3.78 - 4.34: 15772 4.34 - 4.90: 25835 Nonbonded interactions: 60343 Sorted by model distance: nonbonded pdb=" OD2 ASP G 398 " pdb=" OH TYR G 423 " model vdw 2.101 3.040 nonbonded pdb=" O6 NAG D 1 " pdb=" O2 FUC D 4 " model vdw 2.166 2.432 nonbonded pdb=" OE2 GLU A 38 " pdb=" OH TYR G 449 " model vdw 2.172 3.040 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 113 " model vdw 2.202 3.040 nonbonded pdb=" NZ LYS A 174 " pdb=" O THR A 496 " model vdw 2.234 3.120 ... (remaining 60338 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: 3.120 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 0.007 0.066 7559 Z= 0.310 Angle : 1.116 47.677 10352 Z= 0.481 Chirality : 0.164 4.255 1162 Planarity : 0.005 0.044 1307 Dihedral : 14.893 107.503 2565 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.15 % Allowed : 3.74 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -3.07 (0.23), residues: 968 helix: -1.57 (0.22), residues: 396 sheet: -1.79 (0.39), residues: 146 loop : -2.52 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 403 TYR 0.020 0.002 TYR A 381 PHE 0.027 0.002 PHE A 400 TRP 0.018 0.002 TRP A 302 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 7548) covalent geometry : angle 0.69291 (10324) SS BOND : bond 0.00360 ( 5) SS BOND : angle 0.69567 ( 10) hydrogen bonds : bond 0.18239 ( 348) hydrogen bonds : angle 6.93952 ( 990) link_BETA1-4 : bond 0.06506 ( 2) link_BETA1-4 : angle 26.91331 ( 6) link_BETA1-6 : bond 0.06608 ( 1) link_BETA1-6 : angle 33.22244 ( 3) link_NAG-ASN : bond 0.00473 ( 3) link_NAG-ASN : angle 5.53742 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.248 Fit side-chains REVERT: A 38 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6434 (tp30) REVERT: A 63 ASN cc_start: 0.6201 (m110) cc_final: 0.5989 (m110) REVERT: A 455 MET cc_start: 0.7568 (tmm) cc_final: 0.7319 (tmt) REVERT: G 340 GLU cc_start: 0.7048 (mp0) cc_final: 0.6675 (mp0) REVERT: B 91 SER cc_start: 0.8499 (p) cc_final: 0.8226 (t) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.4333 time to fit residues: 66.7113 Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 330 ASN A 442 GLN A 493 HIS G 422 ASN B 37 GLN C 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.121075 restraints weight = 10990.324| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.66 r_work: 0.3594 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7559 Z= 0.146 Angle : 0.644 11.106 10352 Z= 0.315 Chirality : 0.044 0.249 1162 Planarity : 0.005 0.040 1307 Dihedral : 9.350 76.943 1176 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.39 % Allowed : 12.86 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -1.78 (0.25), residues: 968 helix: -0.21 (0.25), residues: 392 sheet: -1.45 (0.38), residues: 154 loop : -1.96 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 403 TYR 0.025 0.002 TYR A 385 PHE 0.016 0.002 PHE B 87 TRP 0.008 0.001 TRP G 436 HIS 0.003 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7548) covalent geometry : angle 0.60443 (10324) SS BOND : bond 0.00716 ( 5) SS BOND : angle 0.75104 ( 10) hydrogen bonds : bond 0.05225 ( 348) hydrogen bonds : angle 5.19039 ( 990) link_BETA1-4 : bond 0.00697 ( 2) link_BETA1-4 : angle 6.34546 ( 6) link_BETA1-6 : bond 0.00168 ( 1) link_BETA1-6 : angle 2.00585 ( 3) link_NAG-ASN : bond 0.00424 ( 3) link_NAG-ASN : angle 5.39116 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.253 Fit side-chains REVERT: A 63 ASN cc_start: 0.6341 (m110) cc_final: 0.5959 (m110) REVERT: A 359 LYS cc_start: 0.7823 (ttpp) cc_final: 0.7464 (tptt) REVERT: A 409 SER cc_start: 0.7665 (p) cc_final: 0.7256 (m) REVERT: A 492 PRO cc_start: 0.7961 (Cg_exo) cc_final: 0.7731 (Cg_endo) REVERT: A 588 PHE cc_start: 0.7731 (m-80) cc_final: 0.7322 (m-80) REVERT: G 470 THR cc_start: 0.8398 (t) cc_final: 0.8159 (t) REVERT: G 503 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8349 (t) REVERT: G 513 LEU cc_start: 0.7937 (mt) cc_final: 0.7733 (mp) REVERT: B 58 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7059 (pt) outliers start: 16 outliers final: 3 residues processed: 136 average time/residue: 0.3935 time to fit residues: 57.5536 Evaluate side-chains 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain B residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 90 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 57 optimal weight: 0.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN A 322 ASN A 374 HIS A 524 GLN G 422 ASN ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.134596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123387 restraints weight = 10831.467| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.66 r_work: 0.3628 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7559 Z= 0.121 Angle : 0.584 9.914 10352 Z= 0.284 Chirality : 0.042 0.201 1162 Planarity : 0.004 0.041 1307 Dihedral : 6.245 44.395 1176 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.84 % Allowed : 16.14 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -1.12 (0.26), residues: 968 helix: 0.44 (0.25), residues: 391 sheet: -1.11 (0.41), residues: 148 loop : -1.71 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.022 0.001 TYR A 385 PHE 0.019 0.001 PHE A 285 TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7548) covalent geometry : angle 0.55356 (10324) SS BOND : bond 0.00397 ( 5) SS BOND : angle 0.72834 ( 10) hydrogen bonds : bond 0.04740 ( 348) hydrogen bonds : angle 4.83874 ( 990) link_BETA1-4 : bond 0.00456 ( 2) link_BETA1-4 : angle 4.87543 ( 6) link_BETA1-6 : bond 0.00493 ( 1) link_BETA1-6 : angle 1.59198 ( 3) link_NAG-ASN : bond 0.00496 ( 3) link_NAG-ASN : angle 4.85986 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: A 63 ASN cc_start: 0.6360 (m110) cc_final: 0.5934 (m110) REVERT: A 359 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7480 (tptt) REVERT: A 376 MET cc_start: 0.8226 (tpp) cc_final: 0.7988 (mtt) REVERT: A 492 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7689 (Cg_endo) REVERT: A 588 PHE cc_start: 0.7736 (m-80) cc_final: 0.7320 (m-80) REVERT: G 453 TYR cc_start: 0.8094 (p90) cc_final: 0.7766 (p90) REVERT: G 470 THR cc_start: 0.8441 (t) cc_final: 0.8152 (t) REVERT: B 58 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7118 (pt) outliers start: 19 outliers final: 7 residues processed: 136 average time/residue: 0.4168 time to fit residues: 60.9525 Evaluate side-chains 132 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 101 GLN G 422 ASN G 493 GLN B 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.134588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123233 restraints weight = 10988.465| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.68 r_work: 0.3626 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7559 Z= 0.127 Angle : 0.570 9.357 10352 Z= 0.279 Chirality : 0.041 0.210 1162 Planarity : 0.004 0.040 1307 Dihedral : 5.274 30.422 1176 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.54 % Allowed : 18.39 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.81 (0.26), residues: 968 helix: 0.65 (0.25), residues: 393 sheet: -0.82 (0.41), residues: 147 loop : -1.54 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.021 0.001 TYR A 385 PHE 0.019 0.001 PHE A 285 TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7548) covalent geometry : angle 0.53972 (10324) SS BOND : bond 0.00266 ( 5) SS BOND : angle 1.04309 ( 10) hydrogen bonds : bond 0.04613 ( 348) hydrogen bonds : angle 4.72180 ( 990) link_BETA1-4 : bond 0.00310 ( 2) link_BETA1-4 : angle 4.68550 ( 6) link_BETA1-6 : bond 0.00290 ( 1) link_BETA1-6 : angle 1.53551 ( 3) link_NAG-ASN : bond 0.00442 ( 3) link_NAG-ASN : angle 4.80033 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.270 Fit side-chains REVERT: A 38 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6731 (tp30) REVERT: A 42 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7294 (mp-120) REVERT: A 63 ASN cc_start: 0.6409 (m110) cc_final: 0.5991 (m110) REVERT: A 359 LYS cc_start: 0.7758 (ttpp) cc_final: 0.7482 (tptt) REVERT: A 588 PHE cc_start: 0.7727 (m-80) cc_final: 0.7290 (m-80) REVERT: G 449 TYR cc_start: 0.8172 (m-80) cc_final: 0.7880 (m-80) REVERT: G 470 THR cc_start: 0.8471 (t) cc_final: 0.8166 (t) REVERT: B 58 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7113 (pt) REVERT: C 54 TYR cc_start: 0.8101 (t80) cc_final: 0.7787 (t80) outliers start: 17 outliers final: 7 residues processed: 131 average time/residue: 0.3883 time to fit residues: 54.7426 Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain C residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 101 GLN A 330 ASN A 374 HIS A 572 HIS G 422 ASN B 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.133322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.121989 restraints weight = 10807.389| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.66 r_work: 0.3611 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.004 0.033 7559 Z= 0.178 Angle : 0.604 8.735 10352 Z= 0.298 Chirality : 0.043 0.226 1162 Planarity : 0.004 0.044 1307 Dihedral : 5.126 30.862 1176 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.14 % Allowed : 20.33 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.68 (0.27), residues: 968 helix: 0.62 (0.26), residues: 397 sheet: -0.59 (0.41), residues: 152 loop : -1.40 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.021 0.002 TYR A 385 PHE 0.021 0.002 PHE A 285 TRP 0.011 0.002 TRP C 36 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7548) covalent geometry : angle 0.57662 (10324) SS BOND : bond 0.00252 ( 5) SS BOND : angle 1.32732 ( 10) hydrogen bonds : bond 0.05057 ( 348) hydrogen bonds : angle 4.75208 ( 990) link_BETA1-4 : bond 0.00194 ( 2) link_BETA1-4 : angle 4.51940 ( 6) link_BETA1-6 : bond 0.00313 ( 1) link_BETA1-6 : angle 1.66530 ( 3) link_NAG-ASN : bond 0.00303 ( 3) link_NAG-ASN : angle 4.69718 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.273 Fit side-chains REVERT: A 63 ASN cc_start: 0.6492 (m110) cc_final: 0.6048 (m110) REVERT: A 588 PHE cc_start: 0.7737 (m-80) cc_final: 0.7299 (m-80) REVERT: B 58 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7068 (pt) REVERT: C 54 TYR cc_start: 0.8131 (t80) cc_final: 0.7842 (t80) outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 0.3649 time to fit residues: 49.7974 Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain C residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 330 ASN G 422 ASN B 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.122913 restraints weight = 10873.938| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.67 r_work: 0.3623 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7559 Z= 0.154 Angle : 0.590 8.817 10352 Z= 0.290 Chirality : 0.042 0.213 1162 Planarity : 0.004 0.043 1307 Dihedral : 4.977 30.315 1176 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.99 % Allowed : 20.48 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.58 (0.27), residues: 968 helix: 0.68 (0.26), residues: 402 sheet: -0.72 (0.40), residues: 162 loop : -1.28 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.020 0.001 TYR A 385 PHE 0.023 0.002 PHE A 285 TRP 0.010 0.001 TRP C 36 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7548) covalent geometry : angle 0.56458 (10324) SS BOND : bond 0.00324 ( 5) SS BOND : angle 1.25110 ( 10) hydrogen bonds : bond 0.04907 ( 348) hydrogen bonds : angle 4.74427 ( 990) link_BETA1-4 : bond 0.00258 ( 2) link_BETA1-4 : angle 4.36639 ( 6) link_BETA1-6 : bond 0.00271 ( 1) link_BETA1-6 : angle 1.57693 ( 3) link_NAG-ASN : bond 0.00268 ( 3) link_NAG-ASN : angle 4.46038 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.279 Fit side-chains REVERT: A 42 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: A 63 ASN cc_start: 0.6521 (m110) cc_final: 0.6071 (m110) REVERT: A 107 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8473 (t) REVERT: A 359 LYS cc_start: 0.7786 (ttpp) cc_final: 0.7406 (tptt) REVERT: A 588 PHE cc_start: 0.7723 (m-80) cc_final: 0.7331 (m-80) REVERT: B 58 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7060 (pt) REVERT: C 54 TYR cc_start: 0.8111 (t80) cc_final: 0.7888 (t80) outliers start: 20 outliers final: 9 residues processed: 132 average time/residue: 0.3841 time to fit residues: 54.8738 Evaluate side-chains 128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain G residue 487 ASN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.0020 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 0.0040 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 374 HIS A 572 HIS G 422 ASN G 439 ASN B 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.136360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124996 restraints weight = 10885.904| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.69 r_work: 0.3651 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7559 Z= 0.113 Angle : 0.564 8.949 10352 Z= 0.277 Chirality : 0.041 0.185 1162 Planarity : 0.004 0.043 1307 Dihedral : 4.755 29.541 1176 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.84 % Allowed : 21.82 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.40 (0.27), residues: 968 helix: 0.82 (0.26), residues: 402 sheet: -0.37 (0.43), residues: 146 loop : -1.28 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.021 0.001 TYR A 41 PHE 0.023 0.001 PHE A 285 TRP 0.008 0.001 TRP A 477 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7548) covalent geometry : angle 0.54082 (10324) SS BOND : bond 0.00253 ( 5) SS BOND : angle 1.12361 ( 10) hydrogen bonds : bond 0.04471 ( 348) hydrogen bonds : angle 4.63200 ( 990) link_BETA1-4 : bond 0.00244 ( 2) link_BETA1-4 : angle 4.22528 ( 6) link_BETA1-6 : bond 0.00251 ( 1) link_BETA1-6 : angle 1.45964 ( 3) link_NAG-ASN : bond 0.00322 ( 3) link_NAG-ASN : angle 4.10489 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7066 (tp30) cc_final: 0.6829 (tp30) REVERT: A 63 ASN cc_start: 0.6526 (m110) cc_final: 0.6072 (m110) REVERT: A 107 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8454 (t) REVERT: A 359 LYS cc_start: 0.7745 (ttpp) cc_final: 0.7378 (tptt) REVERT: A 588 PHE cc_start: 0.7718 (m-80) cc_final: 0.7312 (m-80) REVERT: G 470 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8103 (t) REVERT: B 58 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7066 (pt) outliers start: 19 outliers final: 10 residues processed: 134 average time/residue: 0.4004 time to fit residues: 57.7201 Evaluate side-chains 130 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.0030 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 330 ASN G 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.136573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125191 restraints weight = 10964.644| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.69 r_work: 0.3652 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7559 Z= 0.118 Angle : 0.566 9.240 10352 Z= 0.277 Chirality : 0.041 0.185 1162 Planarity : 0.004 0.040 1307 Dihedral : 4.678 29.590 1176 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.24 % Allowed : 21.97 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.30 (0.27), residues: 968 helix: 0.90 (0.26), residues: 403 sheet: -0.35 (0.43), residues: 146 loop : -1.20 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.018 0.001 TYR A 385 PHE 0.025 0.001 PHE A 285 TRP 0.007 0.001 TRP C 36 HIS 0.007 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7548) covalent geometry : angle 0.54357 (10324) SS BOND : bond 0.00410 ( 5) SS BOND : angle 1.12625 ( 10) hydrogen bonds : bond 0.04381 ( 348) hydrogen bonds : angle 4.57113 ( 990) link_BETA1-4 : bond 0.00265 ( 2) link_BETA1-4 : angle 4.10655 ( 6) link_BETA1-6 : bond 0.00280 ( 1) link_BETA1-6 : angle 1.49268 ( 3) link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 3.97852 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: A 63 ASN cc_start: 0.6506 (m110) cc_final: 0.6059 (m110) REVERT: A 107 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8452 (t) REVERT: A 359 LYS cc_start: 0.7702 (ttpp) cc_final: 0.7380 (tptt) REVERT: A 588 PHE cc_start: 0.7709 (m-80) cc_final: 0.7318 (m-80) REVERT: G 395 VAL cc_start: 0.7360 (OUTLIER) cc_final: 0.7094 (t) REVERT: G 470 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8106 (t) REVERT: B 58 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7074 (pt) REVERT: C 54 TYR cc_start: 0.8092 (t80) cc_final: 0.7881 (t80) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 0.4281 time to fit residues: 59.1367 Evaluate side-chains 135 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 29 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 330 ASN A 374 HIS G 422 ASN B 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.136176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.124723 restraints weight = 10788.575| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.69 r_work: 0.3648 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7559 Z= 0.139 Angle : 0.596 9.680 10352 Z= 0.295 Chirality : 0.042 0.277 1162 Planarity : 0.004 0.039 1307 Dihedral : 4.703 29.896 1176 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.39 % Allowed : 22.72 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.26 (0.27), residues: 968 helix: 0.90 (0.26), residues: 402 sheet: -0.34 (0.42), residues: 152 loop : -1.14 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 340 TYR 0.032 0.001 TYR A 41 PHE 0.026 0.001 PHE A 285 TRP 0.009 0.001 TRP A 477 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7548) covalent geometry : angle 0.56962 (10324) SS BOND : bond 0.00789 ( 5) SS BOND : angle 2.78874 ( 10) hydrogen bonds : bond 0.04482 ( 348) hydrogen bonds : angle 4.63060 ( 990) link_BETA1-4 : bond 0.00275 ( 2) link_BETA1-4 : angle 4.04018 ( 6) link_BETA1-6 : bond 0.00204 ( 1) link_BETA1-6 : angle 1.49962 ( 3) link_NAG-ASN : bond 0.00261 ( 3) link_NAG-ASN : angle 3.93903 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.6541 (m110) cc_final: 0.6093 (m110) REVERT: A 107 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8454 (t) REVERT: A 359 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7359 (tptt) REVERT: A 588 PHE cc_start: 0.7708 (m-80) cc_final: 0.7313 (m-80) REVERT: G 395 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.7111 (t) REVERT: G 470 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8125 (t) REVERT: B 58 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7083 (pt) REVERT: C 54 TYR cc_start: 0.8081 (t80) cc_final: 0.7880 (t80) outliers start: 16 outliers final: 9 residues processed: 130 average time/residue: 0.4329 time to fit residues: 60.4018 Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 330 ASN G 422 ASN B 37 GLN B 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124216 restraints weight = 10792.232| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.69 r_work: 0.3640 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7559 Z= 0.156 Angle : 0.611 10.295 10352 Z= 0.302 Chirality : 0.043 0.287 1162 Planarity : 0.004 0.042 1307 Dihedral : 4.761 30.464 1176 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.09 % Allowed : 23.17 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.26 (0.27), residues: 968 helix: 0.86 (0.26), residues: 403 sheet: -0.36 (0.42), residues: 154 loop : -1.09 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.021 0.002 TYR A 41 PHE 0.027 0.002 PHE A 285 TRP 0.010 0.001 TRP G 436 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7548) covalent geometry : angle 0.58681 (10324) SS BOND : bond 0.00814 ( 5) SS BOND : angle 2.64305 ( 10) hydrogen bonds : bond 0.04619 ( 348) hydrogen bonds : angle 4.64389 ( 990) link_BETA1-4 : bond 0.00236 ( 2) link_BETA1-4 : angle 3.99726 ( 6) link_BETA1-6 : bond 0.00045 ( 1) link_BETA1-6 : angle 1.47355 ( 3) link_NAG-ASN : bond 0.00221 ( 3) link_NAG-ASN : angle 3.96338 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.6579 (m110) cc_final: 0.6120 (m110) REVERT: A 107 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8454 (t) REVERT: A 252 TYR cc_start: 0.8026 (m-80) cc_final: 0.7650 (m-80) REVERT: A 588 PHE cc_start: 0.7711 (m-80) cc_final: 0.7320 (m-80) REVERT: G 395 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7112 (t) REVERT: G 470 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8151 (t) REVERT: B 58 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7113 (pt) REVERT: C 54 TYR cc_start: 0.8074 (t80) cc_final: 0.7857 (t80) outliers start: 14 outliers final: 9 residues processed: 133 average time/residue: 0.4194 time to fit residues: 59.8977 Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 330 ASN G 422 ASN G 439 ASN B 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124531 restraints weight = 10800.260| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.69 r_work: 0.3644 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7559 Z= 0.147 Angle : 0.602 9.912 10352 Z= 0.298 Chirality : 0.042 0.247 1162 Planarity : 0.004 0.039 1307 Dihedral : 4.739 30.387 1176 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.24 % Allowed : 23.47 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.25 (0.27), residues: 968 helix: 0.90 (0.26), residues: 402 sheet: -0.40 (0.42), residues: 154 loop : -1.10 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 340 TYR 0.032 0.002 TYR A 41 PHE 0.028 0.002 PHE A 285 TRP 0.009 0.001 TRP G 436 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7548) covalent geometry : angle 0.57924 (10324) SS BOND : bond 0.00738 ( 5) SS BOND : angle 2.29078 ( 10) hydrogen bonds : bond 0.04576 ( 348) hydrogen bonds : angle 4.63065 ( 990) link_BETA1-4 : bond 0.00214 ( 2) link_BETA1-4 : angle 3.96986 ( 6) link_BETA1-6 : bond 0.00138 ( 1) link_BETA1-6 : angle 1.44452 ( 3) link_NAG-ASN : bond 0.00218 ( 3) link_NAG-ASN : angle 3.90959 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.75 seconds wall clock time: 43 minutes 6.80 seconds (2586.80 seconds total)