Starting phenix.real_space_refine on Wed Mar 4 10:59:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbi_21590/03_2026/6wbi_21590.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbi_21590/03_2026/6wbi_21590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wbi_21590/03_2026/6wbi_21590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbi_21590/03_2026/6wbi_21590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wbi_21590/03_2026/6wbi_21590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbi_21590/03_2026/6wbi_21590.map" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 35 5.16 5 C 8139 2.51 5 N 2392 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13018 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1835 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 777 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 12, 'TYR:plan': 13, 'ASP:plan': 12, 'PHE:plan': 15, 'ASN:plan1': 11, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 373 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1835 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 13, 'TRANS': 309} Chain breaks: 2 Unresolved non-hydrogen bonds: 777 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 12, 'TYR:plan': 13, 'ASP:plan': 12, 'PHE:plan': 15, 'ASN:plan1': 11, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 373 Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1860 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 13, 'TRANS': 313} Chain breaks: 2 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 1000 Unresolved non-hydrogen dihedrals: 639 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 13, 'TYR:plan': 13, 'ASP:plan': 12, 'PHE:plan': 15, 'ASN:plan1': 11, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 377 Chain: "D" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 1846 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 13, 'TRANS': 311} Chain breaks: 2 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 13, 'TYR:plan': 13, 'ASP:plan': 12, 'PHE:plan': 15, 'ASN:plan1': 11, 'ARG:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "E" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 1870 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 793 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 13, 'TYR:plan': 13, 'ASP:plan': 12, 'ARG:plan': 7, 'PHE:plan': 15, 'ASN:plan1': 11, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 382 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 1870 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 793 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 13, 'TYR:plan': 13, 'ASP:plan': 12, 'ARG:plan': 7, 'PHE:plan': 15, 'ASN:plan1': 11, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 382 Chain: "G" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1861 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 799 Unresolved non-hydrogen angles: 1019 Unresolved non-hydrogen dihedrals: 652 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 13, 'TYR:plan': 13, 'ASP:plan': 12, 'ARG:plan': 7, 'PHE:plan': 15, 'ASN:plan1': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 387 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'CBO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.24, per 1000 atoms: 0.25 Number of scatterers: 13018 At special positions: 0 Unit cell: (109.782, 105.678, 123.12, 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 35 16.00 O 2452 8.00 N 2392 7.00 C 8139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.06 Simple disulfide: pdb=" SG CYS C 246 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.05 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: 1.19 Conformation dependent library (CDL) restraints added in 755.6 milliseconds 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 74.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 33 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 99 through 162 removed outlier: 4.087A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix removed outlier: 3.974A pdb=" N ALA A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.154A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.939A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 33 through 55 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 99 through 162 removed outlier: 4.008A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Proline residue: B 133 - end of helix Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 207 through 237 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.052A pdb=" N ASN B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.911A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.924A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.506A pdb=" N SER B 357 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 88 removed outlier: 3.546A pdb=" N VAL C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 4.054A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 162 removed outlier: 3.677A pdb=" N ILE C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 4.915A pdb=" N ALA C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 207 through 237 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.552A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.826A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 358 Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'D' and resid 3 through 14 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 99 through 131 removed outlier: 4.073A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 162 Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 207 through 234 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.003A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.749A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.561A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 Processing helix chain 'E' and resid 32 through 55 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 99 through 130 removed outlier: 4.178A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 130 through 162 removed outlier: 4.396A pdb=" N HIS E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 207 through 237 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.888A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.786A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.886A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 358 Processing helix chain 'E' and resid 361 through 370 Processing helix chain 'F' and resid 3 through 14 removed outlier: 3.739A pdb=" N SER F 13 " --> pdb=" O GLU F 9 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP F 14 " --> pdb=" O TYR F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 99 through 131 removed outlier: 4.102A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.905A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 358 Processing helix chain 'F' and resid 361 through 370 Processing helix chain 'G' and resid 3 through 14 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 99 through 130 removed outlier: 4.269A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 162 Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.700A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 237 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.508A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 326 through 339 removed outlier: 4.323A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 358 Processing helix chain 'G' and resid 361 through 370 removed outlier: 4.196A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.501A pdb=" N GLN D 95 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 245 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.632A pdb=" N SER E 65 " --> pdb=" O LYS E 266 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL E 245 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 4.306A pdb=" N VAL G 245 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN G 95 " --> pdb=" O VAL G 245 " (cutoff:3.500A) 1229 hydrogen bonds defined for protein. 3615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 13191 1.57 - 1.93: 35 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 13227 Sorted by residual: bond pdb=" C LEU B 333 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 1.332 2.996 -1.663 1.40e-02 5.10e+03 1.41e+04 bond pdb=" CA ALA C 131 " pdb=" C ALA C 131 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.37e-02 5.33e+03 9.50e+00 bond pdb=" CA PHE A 244 " pdb=" CB PHE A 244 " ideal model delta sigma weight residual 1.535 1.502 0.034 2.09e-02 2.29e+03 2.60e+00 bond pdb=" CA PHE G 244 " pdb=" CB PHE G 244 " ideal model delta sigma weight residual 1.535 1.505 0.030 1.90e-02 2.77e+03 2.50e+00 bond pdb=" CA GLY C 360 " pdb=" C GLY C 360 " ideal model delta sigma weight residual 1.516 1.528 -0.012 8.20e-03 1.49e+04 2.08e+00 ... (remaining 13222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.67: 18428 15.67 - 31.34: 0 31.34 - 47.01: 0 47.01 - 62.68: 0 62.68 - 78.35: 1 Bond angle restraints: 18429 Sorted by residual: angle pdb=" O LEU B 333 " pdb=" C LEU B 333 " pdb=" N LEU B 335 " ideal model delta sigma weight residual 122.59 44.24 78.35 1.33e+00 5.65e-01 3.47e+03 angle pdb=" C LEU B 333 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 121.54 134.45 -12.91 1.91e+00 2.74e-01 4.57e+01 angle pdb=" N ILE A 311 " pdb=" CA ILE A 311 " pdb=" C ILE A 311 " ideal model delta sigma weight residual 112.80 108.01 4.79 1.15e+00 7.56e-01 1.73e+01 angle pdb=" CA CYS C 265 " pdb=" CB CYS C 265 " pdb=" SG CYS C 265 " ideal model delta sigma weight residual 114.40 122.79 -8.39 2.30e+00 1.89e-01 1.33e+01 angle pdb=" N SER F 239 " pdb=" CA SER F 239 " pdb=" C SER F 239 " ideal model delta sigma weight residual 113.72 108.71 5.01 1.52e+00 4.33e-01 1.09e+01 ... (remaining 18424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 7641 25.53 - 51.05: 89 51.05 - 76.58: 15 76.58 - 102.11: 6 102.11 - 127.63: 5 Dihedral angle restraints: 7756 sinusoidal: 1030 harmonic: 6726 Sorted by residual: dihedral pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta harmonic sigma weight residual 180.00 83.00 97.00 0 5.00e+00 4.00e-02 3.76e+02 dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 265 " pdb=" CB CYS B 265 " ideal model delta sinusoidal sigma weight residual 93.00 19.03 73.97 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 265 " pdb=" CB CYS C 265 " ideal model delta sinusoidal sigma weight residual 93.00 38.56 54.44 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 7753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2298 0.092 - 0.184: 70 0.184 - 0.276: 5 0.276 - 0.368: 1 0.368 - 0.460: 1 Chirality restraints: 2375 Sorted by residual: chirality pdb=" C9 CBO A 401 " pdb=" C10 CBO A 401 " pdb=" C11 CBO A 401 " pdb=" C8 CBO A 401 " both_signs ideal model delta sigma weight residual True 2.68 -2.22 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C10 CBO A 401 " pdb=" C1 CBO A 401 " pdb=" C5 CBO A 401 " pdb=" C9 CBO A 401 " both_signs ideal model delta sigma weight residual True 2.56 -2.84 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA CYS C 66 " pdb=" N CYS C 66 " pdb=" C CYS C 66 " pdb=" CB CYS C 66 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2372 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 333 " -0.147 2.00e-02 2.50e+03 2.58e-01 6.64e+02 pdb=" C LEU B 333 " 0.395 2.00e-02 2.50e+03 pdb=" O LEU B 333 " -0.294 2.00e-02 2.50e+03 pdb=" N LEU B 335 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 74 " 0.016 2.00e-02 2.50e+03 1.24e-02 3.83e+00 pdb=" CG TRP C 74 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C 74 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 74 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 74 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 74 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 74 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 74 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 74 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 123 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 124 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.021 5.00e-02 4.00e+02 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 219 2.67 - 3.23: 15339 3.23 - 3.79: 21669 3.79 - 4.34: 23720 4.34 - 4.90: 36984 Nonbonded interactions: 97931 Sorted by model distance: nonbonded pdb=" O TYR A 331 " pdb=" N LEU A 335 " model vdw 2.117 3.120 nonbonded pdb=" OG SER D 247 " pdb=" O ASP D 261 " model vdw 2.144 3.040 nonbonded pdb=" O TYR C 233 " pdb=" OG SER C 236 " model vdw 2.167 3.040 nonbonded pdb=" OG SER F 247 " pdb=" O ASP F 261 " model vdw 2.172 3.040 nonbonded pdb=" O TYR G 233 " pdb=" OG SER G 236 " model vdw 2.200 3.040 ... (remaining 97926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 133 or (resid 134 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 370)) selection = (chain 'B' and (resid 2 through 133 or (resid 134 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 370)) selection = (chain 'C' and (resid 2 through 30 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'D' and (resid 2 through 14 or resid 32 through 333 or resid 335 through \ 370)) selection = (chain 'E' and (resid 2 through 28 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'F' and (resid 2 through 28 or resid 33 through 133 or (resid 134 through \ 135 and (name N or name CA or name C or name O or name CB )) or resid 136 throu \ gh 333 or resid 335 through 370)) selection = (chain 'G' and (resid 2 through 28 or resid 33 through 333 or resid 335 through \ 370)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.160 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.015 1.663 13235 Z= 1.071 Angle : 0.913 78.352 18445 Z= 0.590 Chirality : 0.043 0.460 2375 Planarity : 0.007 0.258 2522 Dihedral : 10.975 127.634 3296 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 1.00 % Allowed : 7.80 % Favored : 91.20 % 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: -0.82 (0.17), residues: 2238 helix: 0.15 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 75 TYR 0.020 0.001 TYR B 233 PHE 0.020 0.002 PHE D 235 TRP 0.033 0.002 TRP C 74 HIS 0.007 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.01528 (13227) covalent geometry : angle 0.90704 (18429) SS BOND : bond 0.01383 ( 8) SS BOND : angle 3.67294 ( 16) hydrogen bonds : bond 0.13639 ( 1229) hydrogen bonds : angle 5.67293 ( 3615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 SER cc_start: 0.7972 (p) cc_final: 0.7748 (m) REVERT: E 38 VAL cc_start: 0.9335 (t) cc_final: 0.9056 (p) outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.0868 time to fit residues: 15.7969 Evaluate side-chains 74 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 106 HIS A 264 GLN B 76 GLN B 134 HIS C 76 GLN D 76 GLN D 264 GLN E 76 GLN E 106 HIS E 264 GLN F 76 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS G 76 GLN G 264 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.037493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.029012 restraints weight = 165175.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029490 restraints weight = 127771.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.029866 restraints weight = 105377.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.030159 restraints weight = 91027.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030383 restraints weight = 80735.429| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13235 Z= 0.148 Angle : 0.573 8.029 18445 Z= 0.291 Chirality : 0.043 0.454 2375 Planarity : 0.004 0.045 2522 Dihedral : 7.999 131.838 2324 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.80 % Allowed : 5.60 % Favored : 93.60 % 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: 1.41 (0.18), residues: 2240 helix: 1.85 (0.13), residues: 1607 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 75 TYR 0.018 0.001 TYR A 284 PHE 0.013 0.001 PHE G 129 TRP 0.016 0.002 TRP F 74 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00284 (13227) covalent geometry : angle 0.56804 (18429) SS BOND : bond 0.00785 ( 8) SS BOND : angle 2.56193 ( 16) hydrogen bonds : bond 0.03440 ( 1229) hydrogen bonds : angle 4.32414 ( 3615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9167 (m-80) cc_final: 0.8751 (m-80) REVERT: D 284 TYR cc_start: 0.8985 (m-80) cc_final: 0.8731 (m-80) REVERT: E 242 ASP cc_start: 0.9228 (p0) cc_final: 0.8365 (p0) REVERT: G 284 TYR cc_start: 0.8976 (m-80) cc_final: 0.8774 (m-80) outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.0764 time to fit residues: 14.4208 Evaluate side-chains 77 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 60 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 64 optimal weight: 80.0000 chunk 43 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 chunk 217 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 HIS ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.036860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.028665 restraints weight = 168510.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029131 restraints weight = 131778.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.029502 restraints weight = 108860.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.029789 restraints weight = 93560.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029995 restraints weight = 82917.221| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13235 Z= 0.193 Angle : 0.584 7.689 18445 Z= 0.300 Chirality : 0.043 0.462 2375 Planarity : 0.004 0.046 2522 Dihedral : 7.930 129.350 2324 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % 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: 2.00 (0.19), residues: 2240 helix: 2.26 (0.13), residues: 1613 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 75 TYR 0.016 0.001 TYR F 284 PHE 0.020 0.001 PHE G 12 TRP 0.017 0.002 TRP G 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00362 (13227) covalent geometry : angle 0.58015 (18429) SS BOND : bond 0.00649 ( 8) SS BOND : angle 2.46042 ( 16) hydrogen bonds : bond 0.03430 ( 1229) hydrogen bonds : angle 4.17142 ( 3615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9121 (m-80) cc_final: 0.8800 (m-80) REVERT: D 284 TYR cc_start: 0.8926 (m-80) cc_final: 0.8662 (m-80) REVERT: G 242 ASP cc_start: 0.8752 (p0) cc_final: 0.7403 (p0) REVERT: G 284 TYR cc_start: 0.8955 (m-80) cc_final: 0.8725 (m-80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0738 time to fit residues: 13.1852 Evaluate side-chains 72 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 37 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 185 optimal weight: 40.0000 chunk 49 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.036367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.028311 restraints weight = 169898.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.028778 restraints weight = 133556.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029127 restraints weight = 109899.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.029394 restraints weight = 94625.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029617 restraints weight = 84248.323| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13235 Z= 0.225 Angle : 0.610 8.259 18445 Z= 0.319 Chirality : 0.043 0.468 2375 Planarity : 0.004 0.047 2522 Dihedral : 8.003 128.704 2324 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.07 (0.19), residues: 2240 helix: 2.33 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 75 TYR 0.017 0.001 TYR C 284 PHE 0.026 0.001 PHE D 244 TRP 0.016 0.002 TRP F 104 HIS 0.005 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00413 (13227) covalent geometry : angle 0.60588 (18429) SS BOND : bond 0.00595 ( 8) SS BOND : angle 2.44733 ( 16) hydrogen bonds : bond 0.03619 ( 1229) hydrogen bonds : angle 4.25379 ( 3615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9193 (m-10) cc_final: 0.8795 (m-80) REVERT: D 284 TYR cc_start: 0.8974 (m-10) cc_final: 0.8750 (m-80) REVERT: G 242 ASP cc_start: 0.8647 (p0) cc_final: 0.8359 (p0) REVERT: G 284 TYR cc_start: 0.8967 (m-10) cc_final: 0.8715 (m-80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0666 time to fit residues: 10.9357 Evaluate side-chains 70 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 103 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 161 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 177 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 196 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.028904 restraints weight = 168940.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.029379 restraints weight = 130729.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029755 restraints weight = 107423.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.030017 restraints weight = 92088.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.030155 restraints weight = 81919.147| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13235 Z= 0.143 Angle : 0.554 7.926 18445 Z= 0.279 Chirality : 0.042 0.459 2375 Planarity : 0.004 0.051 2522 Dihedral : 7.853 132.729 2324 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 2.56 (0.19), residues: 2240 helix: 2.70 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -1.16 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 75 TYR 0.013 0.001 TYR F 284 PHE 0.016 0.001 PHE E 235 TRP 0.014 0.001 TRP F 104 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00275 (13227) covalent geometry : angle 0.55118 (18429) SS BOND : bond 0.00647 ( 8) SS BOND : angle 1.95766 ( 16) hydrogen bonds : bond 0.02982 ( 1229) hydrogen bonds : angle 3.86317 ( 3615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9136 (m-10) cc_final: 0.8764 (m-80) REVERT: D 284 TYR cc_start: 0.8891 (m-10) cc_final: 0.8544 (m-80) REVERT: F 58 ILE cc_start: 0.6959 (mm) cc_final: 0.6621 (mm) REVERT: G 242 ASP cc_start: 0.8627 (p0) cc_final: 0.8344 (p0) REVERT: G 284 TYR cc_start: 0.8937 (m-10) cc_final: 0.8709 (m-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0713 time to fit residues: 11.7212 Evaluate side-chains 77 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 10.0000 chunk 172 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 174 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 138 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 187 optimal weight: 0.0570 overall best weight: 7.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.036626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.028594 restraints weight = 168510.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.029063 restraints weight = 131040.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.029432 restraints weight = 108020.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029710 restraints weight = 92875.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.029843 restraints weight = 82289.021| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13235 Z= 0.187 Angle : 0.578 8.454 18445 Z= 0.297 Chirality : 0.042 0.468 2375 Planarity : 0.004 0.049 2522 Dihedral : 7.871 130.225 2324 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 2.52 (0.19), residues: 2240 helix: 2.69 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 75 TYR 0.013 0.001 TYR C 284 PHE 0.013 0.001 PHE G 12 TRP 0.015 0.002 TRP F 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00350 (13227) covalent geometry : angle 0.57525 (18429) SS BOND : bond 0.00701 ( 8) SS BOND : angle 2.07063 ( 16) hydrogen bonds : bond 0.03234 ( 1229) hydrogen bonds : angle 3.92570 ( 3615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9158 (m-10) cc_final: 0.8778 (m-80) REVERT: D 284 TYR cc_start: 0.8941 (m-10) cc_final: 0.8740 (m-80) REVERT: G 284 TYR cc_start: 0.8937 (m-10) cc_final: 0.8675 (m-80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0679 time to fit residues: 11.2496 Evaluate side-chains 76 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 135 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 139 optimal weight: 6.9990 chunk 75 optimal weight: 0.0050 chunk 95 optimal weight: 30.0000 chunk 213 optimal weight: 4.9990 chunk 100 optimal weight: 0.0040 chunk 149 optimal weight: 40.0000 chunk 92 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 209 optimal weight: 30.0000 overall best weight: 3.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.037323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.029249 restraints weight = 166281.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.029737 restraints weight = 128294.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030110 restraints weight = 105295.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.030381 restraints weight = 90301.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.030600 restraints weight = 80286.025| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13235 Z= 0.119 Angle : 0.549 8.083 18445 Z= 0.273 Chirality : 0.042 0.458 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.791 134.361 2324 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 2.85 (0.19), residues: 2240 helix: 2.92 (0.13), residues: 1621 sheet: None (None), residues: 0 loop : -1.08 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 75 TYR 0.021 0.001 TYR F 284 PHE 0.016 0.001 PHE G 129 TRP 0.016 0.001 TRP F 74 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00236 (13227) covalent geometry : angle 0.54672 (18429) SS BOND : bond 0.00757 ( 8) SS BOND : angle 1.84555 ( 16) hydrogen bonds : bond 0.02715 ( 1229) hydrogen bonds : angle 3.64061 ( 3615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.9037 (pp20) cc_final: 0.8651 (pp20) REVERT: A 284 TYR cc_start: 0.9097 (m-10) cc_final: 0.8755 (m-80) REVERT: D 284 TYR cc_start: 0.8889 (m-10) cc_final: 0.8516 (m-80) REVERT: G 75 ARG cc_start: 0.8679 (mmt90) cc_final: 0.8312 (mmt90) REVERT: G 284 TYR cc_start: 0.8855 (m-10) cc_final: 0.8635 (m-80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0664 time to fit residues: 11.3766 Evaluate side-chains 78 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 104 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 176 optimal weight: 0.0170 chunk 4 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.037472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.029383 restraints weight = 164475.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.029869 restraints weight = 127541.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.030241 restraints weight = 104822.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.030530 restraints weight = 89950.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030735 restraints weight = 79935.249| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13235 Z= 0.116 Angle : 0.549 8.041 18445 Z= 0.271 Chirality : 0.042 0.466 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.723 133.835 2324 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 3.00 (0.19), residues: 2240 helix: 3.02 (0.13), residues: 1622 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 75 TYR 0.007 0.001 TYR C 284 PHE 0.029 0.001 PHE G 129 TRP 0.013 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00233 (13227) covalent geometry : angle 0.54651 (18429) SS BOND : bond 0.00615 ( 8) SS BOND : angle 1.75493 ( 16) hydrogen bonds : bond 0.02607 ( 1229) hydrogen bonds : angle 3.51574 ( 3615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9083 (m-10) cc_final: 0.8691 (m-80) REVERT: D 284 TYR cc_start: 0.8922 (m-10) cc_final: 0.8582 (m-80) REVERT: G 75 ARG cc_start: 0.8762 (mmt90) cc_final: 0.8509 (mmt90) REVERT: G 272 ILE cc_start: 0.9550 (mp) cc_final: 0.9344 (tp) REVERT: G 284 TYR cc_start: 0.8850 (m-10) cc_final: 0.8626 (m-80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0687 time to fit residues: 11.6710 Evaluate side-chains 75 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 88 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 16 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 188 optimal weight: 30.0000 chunk 214 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.029093 restraints weight = 168867.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.029569 restraints weight = 130002.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.029954 restraints weight = 106680.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030242 restraints weight = 91317.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.030473 restraints weight = 80710.746| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13235 Z= 0.135 Angle : 0.565 10.314 18445 Z= 0.281 Chirality : 0.042 0.466 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.756 133.064 2324 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 2.99 (0.19), residues: 2240 helix: 3.01 (0.13), residues: 1621 sheet: None (None), residues: 0 loop : -1.00 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 75 TYR 0.027 0.001 TYR F 284 PHE 0.026 0.001 PHE G 129 TRP 0.013 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00266 (13227) covalent geometry : angle 0.56205 (18429) SS BOND : bond 0.00509 ( 8) SS BOND : angle 1.93295 ( 16) hydrogen bonds : bond 0.02701 ( 1229) hydrogen bonds : angle 3.57452 ( 3615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9086 (m-10) cc_final: 0.8694 (m-80) REVERT: D 284 TYR cc_start: 0.8970 (m-10) cc_final: 0.8640 (m-80) REVERT: G 75 ARG cc_start: 0.8800 (mmt90) cc_final: 0.8433 (mmt90) REVERT: G 272 ILE cc_start: 0.9547 (mp) cc_final: 0.9339 (tp) REVERT: G 284 TYR cc_start: 0.8879 (m-10) cc_final: 0.8603 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0741 time to fit residues: 11.8121 Evaluate side-chains 77 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 49 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 30.0000 chunk 188 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 202 optimal weight: 5.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.037465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029363 restraints weight = 167694.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029847 restraints weight = 129497.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.030240 restraints weight = 106285.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030534 restraints weight = 90766.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.030752 restraints weight = 80265.174| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13235 Z= 0.113 Angle : 0.553 8.388 18445 Z= 0.271 Chirality : 0.042 0.465 2375 Planarity : 0.004 0.051 2522 Dihedral : 7.724 134.610 2324 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 2240 helix: 3.06 (0.13), residues: 1622 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG E 75 TYR 0.006 0.001 TYR D 230 PHE 0.026 0.001 PHE G 129 TRP 0.012 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00230 (13227) covalent geometry : angle 0.54990 (18429) SS BOND : bond 0.00571 ( 8) SS BOND : angle 1.93108 ( 16) hydrogen bonds : bond 0.02535 ( 1229) hydrogen bonds : angle 3.45973 ( 3615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9101 (m-10) cc_final: 0.8709 (m-80) REVERT: D 284 TYR cc_start: 0.8950 (m-10) cc_final: 0.8622 (m-80) REVERT: E 240 LEU cc_start: 0.9531 (mt) cc_final: 0.9251 (mt) REVERT: G 75 ARG cc_start: 0.8798 (mmt90) cc_final: 0.8509 (mpp80) REVERT: G 272 ILE cc_start: 0.9535 (mp) cc_final: 0.9335 (tp) REVERT: G 284 TYR cc_start: 0.8884 (m-10) cc_final: 0.8630 (m-80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0730 time to fit residues: 11.9880 Evaluate side-chains 77 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 97 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 149 optimal weight: 50.0000 chunk 94 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 51 optimal weight: 0.2980 chunk 116 optimal weight: 6.9990 chunk 187 optimal weight: 0.4980 chunk 200 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.037331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.029310 restraints weight = 167587.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029796 restraints weight = 129526.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.030169 restraints weight = 106367.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030462 restraints weight = 91236.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.030685 restraints weight = 80741.147| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13235 Z= 0.123 Angle : 0.557 8.089 18445 Z= 0.274 Chirality : 0.042 0.466 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.718 133.827 2324 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.08 (0.19), residues: 2240 helix: 3.08 (0.13), residues: 1618 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 75 TYR 0.043 0.001 TYR B 284 PHE 0.025 0.001 PHE G 129 TRP 0.021 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00245 (13227) covalent geometry : angle 0.55419 (18429) SS BOND : bond 0.00515 ( 8) SS BOND : angle 1.90855 ( 16) hydrogen bonds : bond 0.02623 ( 1229) hydrogen bonds : angle 3.49235 ( 3615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1591.32 seconds wall clock time: 28 minutes 8.80 seconds (1688.80 seconds total)