Starting phenix.real_space_refine on Thu Jul 31 03:54:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbi_21590/07_2025/6wbi_21590.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbi_21590/07_2025/6wbi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wbi_21590/07_2025/6wbi_21590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbi_21590/07_2025/6wbi_21590.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbi_21590/07_2025/6wbi_21590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbi_21590/07_2025/6wbi_21590.cif" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 6} 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, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 6} 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, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 6} 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, 'HIS:plan': 2, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 6} 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, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} 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, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} 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, 'HIS:plan': 2, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 13, 'ARG:plan': 7} 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: 9.89, per 1000 atoms: 0.76 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: 5.73 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 1.76 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: 4.61 Time building geometry restraints manager: 5.05 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: 180.210 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.250 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.980 ------------------------------------------------------------------------------- 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 : 12.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.033 0.002 TRP C 74 HIS 0.007 0.001 HIS F 106 PHE 0.020 0.002 PHE D 235 TYR 0.020 0.001 TYR B 233 ARG 0.004 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.13639 ( 1229) hydrogen bonds : angle 5.67293 ( 3615) SS BOND : bond 0.01383 ( 8) SS BOND : angle 3.67294 ( 16) covalent geometry : bond 0.01528 (13227) covalent geometry : angle 0.90704 (18429) *********************** 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 : 1.748 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: 0.2249 time to fit residues: 41.7573 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 : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 175 optimal weight: 50.0000 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 134 HIS C 76 GLN D 76 GLN ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.028978 restraints weight = 165517.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029456 restraints weight = 128371.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.029844 restraints weight = 105908.101| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13235 Z= 0.154 Angle : 0.575 7.984 18445 Z= 0.293 Chirality : 0.043 0.453 2375 Planarity : 0.004 0.044 2522 Dihedral : 8.013 131.537 2324 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.80 % Allowed : 6.00 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2240 helix: 1.84 (0.13), residues: 1607 sheet: None (None), residues: 0 loop : -1.56 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 74 HIS 0.004 0.001 HIS F 106 PHE 0.014 0.001 PHE G 129 TYR 0.017 0.001 TYR A 284 ARG 0.004 0.001 ARG G 75 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1229) hydrogen bonds : angle 4.35100 ( 3615) SS BOND : bond 0.00917 ( 8) SS BOND : angle 2.69796 ( 16) covalent geometry : bond 0.00295 (13227) covalent geometry : angle 0.57019 (18429) *********************** 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 112 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9205 (m-80) cc_final: 0.8759 (m-80) REVERT: D 284 TYR cc_start: 0.9003 (m-80) cc_final: 0.8754 (m-80) REVERT: E 242 ASP cc_start: 0.9234 (p0) cc_final: 0.8396 (p0) REVERT: G 284 TYR cc_start: 0.9013 (m-80) cc_final: 0.8810 (m-80) outliers start: 4 outliers final: 3 residues processed: 112 average time/residue: 0.1779 time to fit residues: 33.2470 Evaluate side-chains 75 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 61 optimal weight: 40.0000 chunk 142 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 217 optimal weight: 50.0000 chunk 44 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.036549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.028380 restraints weight = 168697.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.028840 restraints weight = 131869.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.029196 restraints weight = 109318.341| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13235 Z= 0.225 Angle : 0.607 8.229 18445 Z= 0.317 Chirality : 0.043 0.466 2375 Planarity : 0.004 0.046 2522 Dihedral : 8.005 127.960 2324 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.18), residues: 2240 helix: 2.14 (0.13), residues: 1613 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 74 HIS 0.005 0.001 HIS F 106 PHE 0.021 0.002 PHE G 12 TYR 0.017 0.001 TYR B 284 ARG 0.002 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 1229) hydrogen bonds : angle 4.31341 ( 3615) SS BOND : bond 0.01033 ( 8) SS BOND : angle 2.66630 ( 16) covalent geometry : bond 0.00415 (13227) covalent geometry : angle 0.60258 (18429) *********************** 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 103 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9232 (m-80) cc_final: 0.8928 (m-80) REVERT: D 284 TYR cc_start: 0.9043 (m-80) cc_final: 0.8795 (m-80) REVERT: G 242 ASP cc_start: 0.8748 (p0) cc_final: 0.7993 (p0) REVERT: G 284 TYR cc_start: 0.9044 (m-80) cc_final: 0.8776 (m-80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2525 time to fit residues: 45.6608 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 : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 62 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 166 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 42 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 96 optimal weight: 50.0000 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2909 r_free = 0.2909 target = 0.036644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.028564 restraints weight = 166663.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.029013 restraints weight = 130600.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.029377 restraints weight = 108437.326| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13235 Z= 0.193 Angle : 0.586 8.037 18445 Z= 0.302 Chirality : 0.043 0.459 2375 Planarity : 0.004 0.047 2522 Dihedral : 7.936 130.827 2324 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.19), residues: 2240 helix: 2.46 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 104 HIS 0.005 0.001 HIS F 106 PHE 0.019 0.001 PHE G 12 TYR 0.013 0.001 TYR B 284 ARG 0.002 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 1229) hydrogen bonds : angle 4.08971 ( 3615) SS BOND : bond 0.00742 ( 8) SS BOND : angle 2.34499 ( 16) covalent geometry : bond 0.00356 (13227) covalent geometry : angle 0.58217 (18429) *********************** 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 96 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9187 (m-80) cc_final: 0.8791 (m-80) REVERT: D 284 TYR cc_start: 0.8950 (m-10) cc_final: 0.8700 (m-80) REVERT: G 242 ASP cc_start: 0.8670 (p0) cc_final: 0.8351 (p0) REVERT: G 284 TYR cc_start: 0.8981 (m-10) cc_final: 0.8745 (m-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1622 time to fit residues: 27.5235 Evaluate side-chains 71 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 26 optimal weight: 5.9990 chunk 91 optimal weight: 40.0000 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** 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 = 0.2921 r_free = 0.2921 target = 0.036991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.028901 restraints weight = 167661.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.029393 restraints weight = 130424.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.029738 restraints weight = 106962.064| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13235 Z= 0.157 Angle : 0.559 7.860 18445 Z= 0.283 Chirality : 0.043 0.463 2375 Planarity : 0.004 0.049 2522 Dihedral : 7.864 131.653 2324 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.19), residues: 2240 helix: 2.69 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 104 HIS 0.004 0.001 HIS F 106 PHE 0.017 0.001 PHE E 235 TYR 0.018 0.001 TYR F 284 ARG 0.002 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 1229) hydrogen bonds : angle 3.86813 ( 3615) SS BOND : bond 0.00795 ( 8) SS BOND : angle 2.10103 ( 16) covalent geometry : bond 0.00300 (13227) covalent geometry : angle 0.55620 (18429) *********************** 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 95 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9150 (m-10) cc_final: 0.8787 (m-80) REVERT: D 284 TYR cc_start: 0.8922 (m-10) cc_final: 0.8546 (m-80) REVERT: G 284 TYR cc_start: 0.8965 (m-10) cc_final: 0.8742 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1684 time to fit residues: 27.4145 Evaluate side-chains 73 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 184 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 211 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 19 optimal weight: 0.0670 chunk 10 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- 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 = 0.037488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.029323 restraints weight = 167700.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.029817 restraints weight = 129258.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030195 restraints weight = 106017.980| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13235 Z= 0.117 Angle : 0.545 9.235 18445 Z= 0.269 Chirality : 0.042 0.460 2375 Planarity : 0.004 0.052 2522 Dihedral : 7.777 134.167 2324 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.19), residues: 2240 helix: 2.88 (0.13), residues: 1619 sheet: None (None), residues: 0 loop : -1.08 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 104 HIS 0.005 0.001 HIS F 106 PHE 0.017 0.001 PHE G 129 TYR 0.010 0.001 TYR E 230 ARG 0.002 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.02687 ( 1229) hydrogen bonds : angle 3.61716 ( 3615) SS BOND : bond 0.00957 ( 8) SS BOND : angle 1.87686 ( 16) covalent geometry : bond 0.00234 (13227) covalent geometry : angle 0.54247 (18429) *********************** 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 97 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9109 (m-10) cc_final: 0.8744 (m-80) REVERT: D 284 TYR cc_start: 0.8921 (m-10) cc_final: 0.8538 (m-80) REVERT: G 284 TYR cc_start: 0.8890 (m-10) cc_final: 0.8680 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1664 time to fit residues: 27.9251 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 : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 203 optimal weight: 6.9990 chunk 68 optimal weight: 40.0000 chunk 166 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.2924 r_free = 0.2924 target = 0.037108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.029056 restraints weight = 167770.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029523 restraints weight = 130710.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.029899 restraints weight = 107667.484| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3076 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= 0.145 Angle : 0.562 9.713 18445 Z= 0.281 Chirality : 0.042 0.470 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.780 131.832 2324 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.19), residues: 2240 helix: 2.89 (0.13), residues: 1621 sheet: None (None), residues: 0 loop : -1.06 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 PHE 0.017 0.001 PHE G 129 TYR 0.010 0.001 TYR C 284 ARG 0.007 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 1229) hydrogen bonds : angle 3.65479 ( 3615) SS BOND : bond 0.00736 ( 8) SS BOND : angle 2.25563 ( 16) covalent geometry : bond 0.00283 (13227) covalent geometry : angle 0.55836 (18429) *********************** 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 93 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9100 (m-10) cc_final: 0.8719 (m-80) REVERT: D 284 TYR cc_start: 0.8971 (m-10) cc_final: 0.8644 (m-80) REVERT: G 75 ARG cc_start: 0.8734 (mmt90) cc_final: 0.8383 (mmt90) REVERT: G 272 ILE cc_start: 0.9552 (mp) cc_final: 0.9339 (tp) REVERT: G 284 TYR cc_start: 0.8904 (m-10) cc_final: 0.8634 (m-80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1678 time to fit residues: 27.2830 Evaluate side-chains 71 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 5.9990 chunk 223 optimal weight: 50.0000 chunk 164 optimal weight: 0.0270 chunk 174 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 168 optimal weight: 0.0000 chunk 190 optimal weight: 0.7980 chunk 193 optimal weight: 30.0000 chunk 191 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 overall best weight: 2.5646 ------------------------------------------------------------------------------- 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 = 0.2943 r_free = 0.2943 target = 0.037709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.029576 restraints weight = 166579.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.030021 restraints weight = 128449.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030428 restraints weight = 106618.176| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3357 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= 0.106 Angle : 0.546 9.483 18445 Z= 0.266 Chirality : 0.042 0.456 2375 Planarity : 0.004 0.052 2522 Dihedral : 7.711 135.549 2324 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.19), residues: 2240 helix: 3.03 (0.13), residues: 1622 sheet: None (None), residues: 0 loop : -0.99 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 74 HIS 0.004 0.001 HIS F 106 PHE 0.014 0.001 PHE G 129 TYR 0.024 0.001 TYR F 284 ARG 0.005 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.02485 ( 1229) hydrogen bonds : angle 3.45087 ( 3615) SS BOND : bond 0.00612 ( 8) SS BOND : angle 2.11894 ( 16) covalent geometry : bond 0.00216 (13227) covalent geometry : angle 0.54228 (18429) *********************** 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 101 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9082 (m-10) cc_final: 0.8725 (m-80) REVERT: D 284 TYR cc_start: 0.8966 (m-10) cc_final: 0.8621 (m-80) REVERT: G 75 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8423 (mmt90) REVERT: G 272 ILE cc_start: 0.9521 (mp) cc_final: 0.9309 (tp) REVERT: G 284 TYR cc_start: 0.8882 (m-10) cc_final: 0.8643 (m-80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2103 time to fit residues: 35.6802 Evaluate side-chains 74 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 0.4980 chunk 128 optimal weight: 40.0000 chunk 144 optimal weight: 50.0000 chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 40.0000 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 170 optimal weight: 20.0000 chunk 63 optimal weight: 50.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- 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 = 0.2917 r_free = 0.2917 target = 0.036878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.028855 restraints weight = 168743.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.029313 restraints weight = 131326.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.029684 restraints weight = 108412.978| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13235 Z= 0.167 Angle : 0.571 8.300 18445 Z= 0.289 Chirality : 0.043 0.474 2375 Planarity : 0.004 0.070 2522 Dihedral : 7.774 131.071 2324 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.19), residues: 2240 helix: 2.98 (0.13), residues: 1619 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 74 HIS 0.005 0.001 HIS F 106 PHE 0.030 0.001 PHE G 129 TYR 0.017 0.001 TYR C 284 ARG 0.003 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 1229) hydrogen bonds : angle 3.64937 ( 3615) SS BOND : bond 0.00581 ( 8) SS BOND : angle 2.13088 ( 16) covalent geometry : bond 0.00320 (13227) covalent geometry : angle 0.56801 (18429) *********************** 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 90 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9131 (m-10) cc_final: 0.8768 (m-80) REVERT: D 284 TYR cc_start: 0.9009 (m-10) cc_final: 0.8688 (m-80) REVERT: G 75 ARG cc_start: 0.8802 (mmt90) cc_final: 0.8502 (mpp80) REVERT: G 284 TYR cc_start: 0.8946 (m-10) cc_final: 0.8633 (m-80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2003 time to fit residues: 30.9020 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 : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 219 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 76 optimal weight: 40.0000 chunk 55 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.2919 r_free = 0.2919 target = 0.036912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.028884 restraints weight = 167440.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029354 restraints weight = 130523.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.029709 restraints weight = 107811.860| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13235 Z= 0.144 Angle : 0.563 8.561 18445 Z= 0.283 Chirality : 0.043 0.461 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.761 133.461 2324 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.19), residues: 2240 helix: 3.00 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.95 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 PHE 0.026 0.001 PHE G 129 TYR 0.025 0.001 TYR F 284 ARG 0.004 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 1229) hydrogen bonds : angle 3.59947 ( 3615) SS BOND : bond 0.00570 ( 8) SS BOND : angle 2.07487 ( 16) covalent geometry : bond 0.00279 (13227) covalent geometry : angle 0.55971 (18429) ********************** 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 90 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9138 (m-10) cc_final: 0.8751 (m-80) REVERT: D 284 TYR cc_start: 0.9023 (m-10) cc_final: 0.8707 (m-80) REVERT: G 75 ARG cc_start: 0.8820 (mmt90) cc_final: 0.8511 (mpp80) REVERT: G 284 TYR cc_start: 0.8922 (m-10) cc_final: 0.8646 (m-80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1812 time to fit residues: 28.3823 Evaluate side-chains 73 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.2920 r_free = 0.2920 target = 0.036946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.028940 restraints weight = 168931.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029408 restraints weight = 131052.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029786 restraints weight = 107992.762| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13235 Z= 0.143 Angle : 0.562 8.433 18445 Z= 0.282 Chirality : 0.043 0.469 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.759 132.799 2324 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.19), residues: 2240 helix: 3.03 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.92 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 PHE 0.027 0.001 PHE G 129 TYR 0.013 0.001 TYR F 284 ARG 0.004 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 1229) hydrogen bonds : angle 3.59031 ( 3615) SS BOND : bond 0.00552 ( 8) SS BOND : angle 2.04182 ( 16) covalent geometry : bond 0.00277 (13227) covalent geometry : angle 0.55928 (18429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.84 seconds wall clock time: 73 minutes 45.06 seconds (4425.06 seconds total)