Starting phenix.real_space_refine on Mon Dec 30 12:10:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbi_21590/12_2024/6wbi_21590.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbi_21590/12_2024/6wbi_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_21590/12_2024/6wbi_21590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbi_21590/12_2024/6wbi_21590.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbi_21590/12_2024/6wbi_21590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbi_21590/12_2024/6wbi_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.30, per 1000 atoms: 0.71 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: 3.97 Conformation dependent library (CDL) restraints added in 2.2 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: 1.48 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: 4.40 Time building geometry restraints manager: 4.44 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.800 Find NCS groups from input model: 0.750 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- 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 13227 Z= 0.450 Angle : 0.907 78.352 18429 Z= 0.588 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 *********************** 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 : 1.556 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: 0.1937 time to fit residues: 35.4960 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 : 1.631 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 13227 Z= 0.206 Angle : 0.570 7.984 18429 Z= 0.291 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 *********************** 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 : 1.680 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.7642 (m-80) cc_final: 0.7395 (m-80) REVERT: E 38 VAL cc_start: 0.9289 (t) cc_final: 0.9011 (p) REVERT: E 242 ASP cc_start: 0.7999 (p0) cc_final: 0.7038 (p0) outliers start: 4 outliers final: 3 residues processed: 112 average time/residue: 0.1796 time to fit residues: 33.9744 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 : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 138 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 220 optimal weight: 50.0000 chunk 181 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13227 Z= 0.213 Angle : 0.563 8.177 18429 Z= 0.285 Chirality : 0.043 0.459 2375 Planarity : 0.004 0.047 2522 Dihedral : 7.880 130.856 2324 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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 : 0.00 % 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: 2.16 (0.19), residues: 2240 helix: 2.39 (0.13), residues: 1613 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 74 HIS 0.004 0.001 HIS F 106 PHE 0.025 0.001 PHE G 12 TYR 0.019 0.001 TYR F 284 ARG 0.002 0.000 ARG F 75 *********************** 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 108 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 VAL cc_start: 0.9323 (t) cc_final: 0.9068 (p) REVERT: G 242 ASP cc_start: 0.7703 (p0) cc_final: 0.6461 (p0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1938 time to fit residues: 34.8177 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 : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 204 optimal weight: 20.0000 chunk 216 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 chunk 193 optimal weight: 50.0000 chunk 58 optimal weight: 50.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- 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** F 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13227 Z= 0.267 Angle : 0.588 8.065 18429 Z= 0.305 Chirality : 0.043 0.466 2375 Planarity : 0.004 0.047 2522 Dihedral : 7.931 128.952 2324 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 2.34 (0.19), residues: 2240 helix: 2.53 (0.13), residues: 1603 sheet: None (None), residues: 0 loop : -1.12 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 104 HIS 0.005 0.001 HIS F 106 PHE 0.021 0.001 PHE G 12 TYR 0.016 0.001 TYR A 284 ARG 0.003 0.001 ARG B 75 *********************** 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 97 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: G 242 ASP cc_start: 0.7794 (p0) cc_final: 0.7510 (p0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1841 time to fit residues: 30.0650 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 : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 20.0000 chunk 122 optimal weight: 0.0000 chunk 3 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 149 optimal weight: 50.0000 chunk 0 optimal weight: 60.0000 chunk 110 optimal weight: 30.0000 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13227 Z= 0.223 Angle : 0.563 7.797 18429 Z= 0.287 Chirality : 0.042 0.459 2375 Planarity : 0.004 0.047 2522 Dihedral : 7.873 131.453 2324 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 2.50 (0.19), residues: 2240 helix: 2.65 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -1.16 (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 0.016 0.001 PHE G 12 TYR 0.016 0.001 TYR F 284 ARG 0.004 0.001 ARG B 75 *********************** 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 : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1904 time to fit residues: 31.0689 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 : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 113 optimal weight: 8.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13227 Z= 0.186 Angle : 0.553 9.187 18429 Z= 0.277 Chirality : 0.042 0.462 2375 Planarity : 0.004 0.048 2522 Dihedral : 7.819 132.558 2324 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 2.68 (0.19), residues: 2240 helix: 2.78 (0.13), residues: 1617 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 623 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 0.014 0.001 PHE G 129 TYR 0.023 0.001 TYR A 284 ARG 0.008 0.001 ARG E 75 *********************** 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 93 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1707 time to fit residues: 27.5951 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 : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 0.0980 chunk 121 optimal weight: 0.0470 chunk 215 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.5480 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13227 Z= 0.143 Angle : 0.541 8.300 18429 Z= 0.263 Chirality : 0.042 0.455 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.690 136.444 2324 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: 2.98 (0.19), residues: 2240 helix: 3.01 (0.13), residues: 1622 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 618 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 0.000 PHE G 129 TYR 0.039 0.001 TYR F 284 ARG 0.009 0.001 ARG E 75 *********************** 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 99 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 282 VAL cc_start: 0.9698 (t) cc_final: 0.9447 (p) REVERT: G 284 TYR cc_start: 0.7555 (m-80) cc_final: 0.7292 (m-80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1731 time to fit residues: 29.3862 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 : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 40.0000 chunk 65 optimal weight: 40.0000 chunk 42 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13227 Z= 0.165 Angle : 0.548 9.739 18429 Z= 0.269 Chirality : 0.042 0.462 2375 Planarity : 0.004 0.050 2522 Dihedral : 7.680 133.819 2324 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: 3.02 (0.19), residues: 2240 helix: 3.03 (0.13), residues: 1622 sheet: None (None), residues: 0 loop : -1.00 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 74 HIS 0.005 0.001 HIS F 106 PHE 0.030 0.001 PHE G 129 TYR 0.043 0.001 TYR B 284 ARG 0.005 0.001 ARG E 75 *********************** 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 95 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.7620 (m-80) cc_final: 0.7373 (m-80) REVERT: G 284 TYR cc_start: 0.7528 (m-80) cc_final: 0.7278 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1707 time to fit residues: 27.9740 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 : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 50.0000 chunk 206 optimal weight: 90.0000 chunk 188 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 200 optimal weight: 40.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13227 Z= 0.278 Angle : 0.602 8.349 18429 Z= 0.314 Chirality : 0.043 0.473 2375 Planarity : 0.004 0.048 2522 Dihedral : 7.869 129.135 2324 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 2.78 (0.19), residues: 2240 helix: 2.85 (0.13), residues: 1617 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 74 HIS 0.005 0.001 HIS F 106 PHE 0.026 0.001 PHE G 129 TYR 0.016 0.001 TYR C 284 ARG 0.010 0.001 ARG E 75 *********************** 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 88 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.7876 (m-80) cc_final: 0.7632 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1679 time to fit residues: 25.7088 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 : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 223 optimal weight: 50.0000 chunk 205 optimal weight: 40.0000 chunk 177 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13227 Z= 0.203 Angle : 0.567 8.460 18429 Z= 0.286 Chirality : 0.043 0.456 2375 Planarity : 0.004 0.049 2522 Dihedral : 7.799 133.898 2324 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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 (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: 2.87 (0.19), residues: 2240 helix: 2.90 (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 0.019 0.001 TRP F 74 HIS 0.004 0.001 HIS F 106 PHE 0.025 0.001 PHE G 129 TYR 0.027 0.001 TYR D 284 ARG 0.007 0.001 ARG E 75 ********************** 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 88 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: A 284 TYR cc_start: 0.7788 (m-80) cc_final: 0.7534 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1657 time to fit residues: 26.2963 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 : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 40.0000 chunk 189 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.2919 r_free = 0.2919 target = 0.036930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028978 restraints weight = 167245.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.029392 restraints weight = 129890.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029778 restraints weight = 108558.829| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13227 Z= 0.194 Angle : 0.564 8.314 18429 Z= 0.283 Chirality : 0.043 0.469 2375 Planarity : 0.004 0.049 2522 Dihedral : 7.776 132.826 2324 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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: 2.93 (0.19), residues: 2240 helix: 2.94 (0.13), residues: 1621 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 74 HIS 0.005 0.001 HIS F 106 PHE 0.025 0.001 PHE G 129 TYR 0.028 0.001 TYR F 284 ARG 0.002 0.000 ARG G 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.60 seconds wall clock time: 36 minutes 7.08 seconds (2167.08 seconds total)