Starting phenix.real_space_refine on Thu Jun 4 14:12:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqq_61736/06_2026/9jqq_61736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqq_61736/06_2026/9jqq_61736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jqq_61736/06_2026/9jqq_61736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqq_61736/06_2026/9jqq_61736_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqq_61736/06_2026/9jqq_61736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqq_61736/06_2026/9jqq_61736.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.026 sd= 0.287 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 68 5.16 5 C 8669 2.51 5 N 2355 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13654 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3773 Classifications: {'peptide': 476} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2233 Classifications: {'peptide': 290} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "E" Number of atoms: 3750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3750 Classifications: {'peptide': 463} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 434} Chain breaks: 7 Chain: "F" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3743 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 438} Chain breaks: 6 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.11, per 1000 atoms: 0.23 Number of scatterers: 13654 At special positions: 0 Unit cell: (107.35, 145.35, 259.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 2 15.00 O 2560 8.00 N 2355 7.00 C 8669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 191 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 401 " - " ASN B 86 " " NAG C 1 " - " ASN E 18 " " NAG D 1 " - " ASN E 92 " " NAG E 601 " - " ASN E 86 " " NAG E 602 " - " ASN E 188 " " NAG F 601 " - " ASN F 86 " " NAG G 1 " - " ASN E 194 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 615.9 milliseconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3158 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 24 sheets defined 19.7% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 57 through 60 removed outlier: 3.789A pdb=" N GLN A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 219 through 290 removed outlier: 3.640A pdb=" N LEU A 223 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.955A pdb=" N MET A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.909A pdb=" N ARG B 65 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 292 removed outlier: 4.102A pdb=" N ALA B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Proline residue: B 228 - end of helix Processing helix chain 'E' and resid 224 through 294 Proline residue: E 233 - end of helix Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.680A pdb=" N GLY F 53 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.881A pdb=" N ASN F 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 294 Proline residue: F 233 - end of helix removed outlier: 3.597A pdb=" N GLU F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 5.855A pdb=" N ILE A 11 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA A 115 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 13 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 48 " --> pdb=" O TRP A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.443A pdb=" N VAL A 123 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 200 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TRP B 150 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 158 " --> pdb=" O TRP B 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 151 removed outlier: 8.944A pdb=" N VAL B 123 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER A 205 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL B 125 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 207 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY B 127 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL B 123 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG B 138 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL B 125 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU B 136 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY B 127 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N TYR B 173 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 161 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.633A pdb=" N LYS A 309 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 367 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 320 removed outlier: 5.082A pdb=" N LEU A 356 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N LYS A 318 " --> pdb=" O CYS A 354 " (cutoff:3.500A) removed outlier: 11.054A pdb=" N CYS A 354 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 14 removed outlier: 6.326A pdb=" N ILE B 11 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 115 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA B 13 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER B 40 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL B 46 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AB2, first strand: chain 'E' and resid 47 through 50 removed outlier: 5.039A pdb=" N PHE E 48 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP E 38 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY E 93 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 112 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.726A pdb=" N SER E 124 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU E 136 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR E 176 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 164 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA E 178 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.669A pdb=" N LEU E 147 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN E 194 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER E 190 " --> pdb=" O ARG E 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET E 189 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS E 191 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER E 204 " --> pdb=" O CYS E 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 313 through 314 removed outlier: 3.994A pdb=" N PHE E 470 " --> pdb=" O GLU E 363 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 313 through 314 removed outlier: 3.994A pdb=" N PHE E 470 " --> pdb=" O GLU E 363 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS E 298 " --> pdb=" O LYS E 357 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR E 359 " --> pdb=" O HIS E 298 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E 297 " --> pdb=" O ALA F 299 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 346 through 348 Processing sheet with id=AB8, first strand: chain 'E' and resid 488 through 489 removed outlier: 6.678A pdb=" N PHE F 435 " --> pdb=" O ILE F 444 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.864A pdb=" N HIS F 24 " --> pdb=" O VAL F 5 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.477A pdb=" N ILE F 11 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ALA F 115 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA F 13 " --> pdb=" O ALA F 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.906A pdb=" N SER F 124 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU F 136 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AC4, first strand: chain 'F' and resid 313 through 315 removed outlier: 3.824A pdb=" N VAL F 322 " --> pdb=" O ILE F 469 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 469 " --> pdb=" O VAL F 322 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 346 through 348 Processing sheet with id=AC6, first strand: chain 'F' and resid 357 through 358 532 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4462 1.34 - 1.46: 3027 1.46 - 1.58: 6352 1.58 - 1.70: 3 1.70 - 1.82: 101 Bond restraints: 13945 Sorted by residual: bond pdb=" O16 H6P A 601 " pdb=" P17 H6P A 601 " ideal model delta sigma weight residual 1.697 1.619 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" O20 H6P A 601 " pdb=" P17 H6P A 601 " ideal model delta sigma weight residual 1.521 1.486 0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" CA ARG E 40 " pdb=" C ARG E 40 " ideal model delta sigma weight residual 1.524 1.512 0.012 7.00e-03 2.04e+04 2.89e+00 ... (remaining 13940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18249 1.79 - 3.58: 510 3.58 - 5.37: 71 5.37 - 7.16: 23 7.16 - 8.95: 8 Bond angle restraints: 18861 Sorted by residual: angle pdb=" N GLU E 35 " pdb=" CA GLU E 35 " pdb=" C GLU E 35 " ideal model delta sigma weight residual 110.35 117.16 -6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" N ASN B 48 " pdb=" CA ASN B 48 " pdb=" C ASN B 48 " ideal model delta sigma weight residual 108.75 116.68 -7.93 1.71e+00 3.42e-01 2.15e+01 angle pdb=" N SER F 41 " pdb=" CA SER F 41 " pdb=" C SER F 41 " ideal model delta sigma weight residual 114.75 109.08 5.67 1.26e+00 6.30e-01 2.03e+01 angle pdb=" N VAL F 454 " pdb=" CA VAL F 454 " pdb=" C VAL F 454 " ideal model delta sigma weight residual 109.19 106.09 3.10 8.20e-01 1.49e+00 1.43e+01 angle pdb=" C GLN A 251 " pdb=" N PHE A 252 " pdb=" CA PHE A 252 " ideal model delta sigma weight residual 121.14 115.08 6.06 1.75e+00 3.27e-01 1.20e+01 ... (remaining 18856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.23: 8280 29.23 - 58.46: 273 58.46 - 87.69: 21 87.69 - 116.92: 0 116.92 - 146.15: 2 Dihedral angle restraints: 8576 sinusoidal: 3692 harmonic: 4884 Sorted by residual: dihedral pdb=" CB CYS A 137 " pdb=" SG CYS A 137 " pdb=" SG CYS A 191 " pdb=" CB CYS A 191 " ideal model delta sinusoidal sigma weight residual 93.00 159.91 -66.91 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 144.61 -51.61 1 1.00e+01 1.00e-02 3.64e+01 dihedral pdb=" CA SER E 44 " pdb=" C SER E 44 " pdb=" N PRO E 45 " pdb=" CA PRO E 45 " ideal model delta harmonic sigma weight residual 0.00 -27.13 27.13 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 8573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1936 0.090 - 0.180: 156 0.180 - 0.269: 6 0.269 - 0.359: 0 0.359 - 0.449: 1 Chirality restraints: 2099 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN E 92 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CB VAL F 406 " pdb=" CA VAL F 406 " pdb=" CG1 VAL F 406 " pdb=" CG2 VAL F 406 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 148 " pdb=" CA ILE B 148 " pdb=" CG1 ILE B 148 " pdb=" CG2 ILE B 148 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2096 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 38 " -0.025 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP B 38 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 38 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 38 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 38 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 38 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 38 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 38 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 38 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 38 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 150 " -0.024 2.00e-02 2.50e+03 1.88e-02 8.83e+00 pdb=" CG TRP A 150 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 150 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 150 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 150 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 150 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 150 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 150 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 150 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 150 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 240 " -0.017 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP E 240 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP E 240 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 240 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 240 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 240 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 240 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 240 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 240 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 240 " -0.002 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1059 2.74 - 3.28: 13442 3.28 - 3.82: 21820 3.82 - 4.36: 24387 4.36 - 4.90: 42178 Nonbonded interactions: 102886 Sorted by model distance: nonbonded pdb=" OG1 THR F 14 " pdb=" OE2 GLU F 17 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP B 168 " pdb=" N GLY B 169 " model vdw 2.209 3.120 nonbonded pdb=" O ILE E 444 " pdb=" OG1 THR F 489 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR E 88 " pdb=" OE1 GLN E 90 " model vdw 2.224 3.040 nonbonded pdb=" OG SER A 384 " pdb=" OE2 GLU A 463 " model vdw 2.240 3.040 ... (remaining 102881 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 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'E' and (resid 1 through 142 or resid 145 through 164 or resid 171 throug \ h 326 or resid 334 through 485 or resid 487 through 492 or resid 602)) selection = (chain 'F' and (resid 1 through 28 or resid 33 through 129 or resid 134 through \ 154 or resid 158 through 406 or resid 409 through 462 or resid 465 through 601)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.520 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: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.060 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 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 : 0.004 0.078 13963 Z= 0.178 Angle : 0.722 8.947 18907 Z= 0.377 Chirality : 0.047 0.449 2099 Planarity : 0.005 0.050 2409 Dihedral : 13.921 146.148 5394 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 0.27 % Allowed : 0.54 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1652 helix: 3.31 (0.27), residues: 294 sheet: -0.18 (0.23), residues: 483 loop : -1.69 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 138 TYR 0.028 0.002 TYR F 428 PHE 0.013 0.001 PHE A 252 TRP 0.053 0.002 TRP B 38 HIS 0.006 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (13945) covalent geometry : angle 0.71142 / 0.37 (18861) SS BOND : bond 0.00364 / 0.20 ( 8) SS BOND : angle 0.96847 / 0.62 ( 16) hydrogen bonds : bond 0.11044 / 7.50 ( 527) hydrogen bonds : angle 5.49744 / 3.69 ( 1443) link_BETA1-4 : bond 0.01281 / 0.64 ( 3) link_BETA1-4 : angle 4.54616 / 2.81 ( 9) link_NAG-ASN : bond 0.00317 / 0.16 ( 7) link_NAG-ASN : angle 2.17352 / 1.52 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7493 (mtt-85) outliers start: 4 outliers final: 3 residues processed: 271 average time/residue: 0.1708 time to fit residues: 61.1970 Evaluate side-chains 184 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 48 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.062039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.051080 restraints weight = 92862.920| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.40 r_work: 0.3267 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13963 Z= 0.141 Angle : 0.687 10.195 18907 Z= 0.348 Chirality : 0.046 0.245 2099 Planarity : 0.005 0.060 2409 Dihedral : 7.294 106.631 2079 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 1.15 % Allowed : 10.44 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1652 helix: 3.44 (0.26), residues: 294 sheet: 0.04 (0.24), residues: 486 loop : -1.66 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 138 TYR 0.017 0.002 TYR A 95 PHE 0.019 0.002 PHE A 252 TRP 0.030 0.002 TRP B 150 HIS 0.005 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (13945) covalent geometry : angle 0.68049 / 0.35 (18861) SS BOND : bond 0.00893 / 0.46 ( 8) SS BOND : angle 1.27205 / 0.77 ( 16) hydrogen bonds : bond 0.05387 / 3.66 ( 527) hydrogen bonds : angle 4.89776 / 3.35 ( 1443) link_BETA1-4 : bond 0.01106 / 0.55 ( 3) link_BETA1-4 : angle 3.63664 / 2.40 ( 9) link_NAG-ASN : bond 0.00272 / 0.14 ( 7) link_NAG-ASN : angle 1.48398 / 0.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8377 (tpp) cc_final: 0.8160 (tpp) REVERT: A 105 TYR cc_start: 0.8913 (p90) cc_final: 0.8373 (p90) REVERT: A 142 TRP cc_start: 0.6063 (m100) cc_final: 0.5837 (m100) REVERT: A 172 LEU cc_start: 0.8121 (pt) cc_final: 0.7891 (tp) REVERT: A 234 LEU cc_start: 0.8534 (mt) cc_final: 0.8319 (pp) REVERT: A 257 ARG cc_start: 0.8437 (ptp-170) cc_final: 0.8234 (ptt-90) REVERT: A 293 ARG cc_start: 0.5228 (mtt90) cc_final: 0.4701 (mtt-85) REVERT: A 404 MET cc_start: 0.8587 (tmm) cc_final: 0.8367 (ttp) REVERT: B 34 MET cc_start: 0.7551 (mtm) cc_final: 0.7228 (ptp) REVERT: B 37 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8499 (ttpt) REVERT: B 107 LYS cc_start: 0.8334 (ptpp) cc_final: 0.8058 (mtmt) REVERT: E 189 MET cc_start: 0.7305 (tpp) cc_final: 0.7103 (tpt) REVERT: F 22 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6733 (ttp80) REVERT: F 39 PHE cc_start: 0.5770 (p90) cc_final: 0.5169 (p90) REVERT: F 98 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: F 213 MET cc_start: 0.4385 (ttp) cc_final: 0.1011 (tpt) REVERT: F 245 GLN cc_start: 0.8824 (pt0) cc_final: 0.8463 (mm-40) REVERT: F 273 ARG cc_start: 0.8454 (tpp80) cc_final: 0.8221 (tpp80) REVERT: F 307 ASP cc_start: 0.8635 (m-30) cc_final: 0.8387 (t0) REVERT: F 339 GLU cc_start: 0.8628 (pm20) cc_final: 0.8137 (pm20) outliers start: 17 outliers final: 5 residues processed: 206 average time/residue: 0.1527 time to fit residues: 42.2771 Evaluate side-chains 187 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 111 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 141 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 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 = 0.3588 r_free = 0.3588 target = 0.057240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.046650 restraints weight = 94420.719| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.20 r_work: 0.3142 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13963 Z= 0.307 Angle : 0.812 9.355 18907 Z= 0.422 Chirality : 0.049 0.243 2099 Planarity : 0.006 0.060 2409 Dihedral : 7.246 82.314 2071 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 1.83 % Allowed : 15.12 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1652 helix: 2.43 (0.26), residues: 301 sheet: -0.11 (0.23), residues: 472 loop : -1.70 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 83 TYR 0.032 0.003 TYR F 359 PHE 0.033 0.003 PHE A 252 TRP 0.023 0.003 TRP B 38 HIS 0.013 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.31 (13945) covalent geometry : angle 0.80551 / 0.42 (18861) SS BOND : bond 0.01324 / 0.67 ( 8) SS BOND : angle 1.76093 / 1.26 ( 16) hydrogen bonds : bond 0.07322 / 4.88 ( 527) hydrogen bonds : angle 5.30727 / 3.65 ( 1443) link_BETA1-4 : bond 0.00834 / 0.42 ( 3) link_BETA1-4 : angle 3.45493 / 2.37 ( 9) link_NAG-ASN : bond 0.00736 / 0.40 ( 7) link_NAG-ASN : angle 1.97403 / 1.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7592 (m100) cc_final: 0.7358 (m100) REVERT: A 105 TYR cc_start: 0.8812 (p90) cc_final: 0.8336 (p90) REVERT: A 142 TRP cc_start: 0.6329 (m100) cc_final: 0.6117 (m100) REVERT: A 152 ASN cc_start: 0.8866 (m-40) cc_final: 0.8662 (t0) REVERT: A 252 PHE cc_start: 0.8638 (p90) cc_final: 0.8426 (p90) REVERT: A 257 ARG cc_start: 0.8481 (ptp-170) cc_final: 0.8241 (ptt-90) REVERT: A 263 GLU cc_start: 0.8813 (mp0) cc_final: 0.8613 (mm-30) REVERT: A 293 ARG cc_start: 0.5783 (mtt90) cc_final: 0.4855 (mtt-85) REVERT: B 37 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8534 (ttpt) REVERT: B 261 MET cc_start: 0.8027 (tmm) cc_final: 0.7807 (tmm) REVERT: E 57 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8238 (p) REVERT: E 307 ASP cc_start: 0.8734 (t0) cc_final: 0.8445 (t0) REVERT: E 366 ASN cc_start: 0.8699 (p0) cc_final: 0.8421 (p0) REVERT: E 439 ARG cc_start: 0.8800 (tmm-80) cc_final: 0.8499 (tmm-80) REVERT: F 111 HIS cc_start: 0.7404 (t-90) cc_final: 0.7182 (t-90) REVERT: F 213 MET cc_start: 0.4688 (ttp) cc_final: 0.1338 (tpt) REVERT: F 228 VAL cc_start: 0.8887 (t) cc_final: 0.8543 (t) REVERT: F 245 GLN cc_start: 0.8907 (pt0) cc_final: 0.8526 (mm-40) REVERT: F 307 ASP cc_start: 0.8920 (m-30) cc_final: 0.8685 (t0) REVERT: F 339 GLU cc_start: 0.8453 (pm20) cc_final: 0.8062 (pm20) REVERT: F 464 CYS cc_start: 0.8555 (t) cc_final: 0.8330 (m) outliers start: 27 outliers final: 11 residues processed: 214 average time/residue: 0.1571 time to fit residues: 45.5667 Evaluate side-chains 185 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN F 200 GLN ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.058040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047508 restraints weight = 92973.915| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 4.16 r_work: 0.3173 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13963 Z= 0.163 Angle : 0.700 11.718 18907 Z= 0.356 Chirality : 0.045 0.259 2099 Planarity : 0.005 0.051 2409 Dihedral : 6.834 84.649 2068 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 1.69 % Allowed : 17.22 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1652 helix: 2.85 (0.26), residues: 301 sheet: -0.11 (0.23), residues: 483 loop : -1.61 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 138 TYR 0.020 0.002 TYR F 359 PHE 0.033 0.002 PHE A 252 TRP 0.015 0.002 TRP A 150 HIS 0.006 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (13945) covalent geometry : angle 0.69238 / 0.35 (18861) SS BOND : bond 0.01240 / 0.64 ( 8) SS BOND : angle 1.47226 / 0.84 ( 16) hydrogen bonds : bond 0.06437 / 4.28 ( 527) hydrogen bonds : angle 5.04751 / 3.45 ( 1443) link_BETA1-4 : bond 0.01052 / 0.53 ( 3) link_BETA1-4 : angle 3.61648 / 2.40 ( 9) link_NAG-ASN : bond 0.00329 / 0.16 ( 7) link_NAG-ASN : angle 1.75918 / 1.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8748 (p90) cc_final: 0.8322 (p90) REVERT: A 126 LYS cc_start: 0.7609 (pttt) cc_final: 0.7361 (pttp) REVERT: A 142 TRP cc_start: 0.6244 (m100) cc_final: 0.5923 (m100) REVERT: A 252 PHE cc_start: 0.8770 (p90) cc_final: 0.8568 (p90) REVERT: A 257 ARG cc_start: 0.8422 (ptp-170) cc_final: 0.8150 (ptt-90) REVERT: A 263 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: B 37 LYS cc_start: 0.8885 (ttpt) cc_final: 0.8624 (ttpt) REVERT: B 182 ARG cc_start: 0.8865 (mmp80) cc_final: 0.8659 (mmp80) REVERT: B 261 MET cc_start: 0.8008 (tmm) cc_final: 0.7780 (tmm) REVERT: B 266 TYR cc_start: 0.8073 (m-80) cc_final: 0.7854 (m-80) REVERT: E 57 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8202 (p) REVERT: E 307 ASP cc_start: 0.8701 (t0) cc_final: 0.8374 (t0) REVERT: E 314 PHE cc_start: 0.7265 (m-80) cc_final: 0.7049 (m-80) REVERT: E 366 ASN cc_start: 0.8757 (p0) cc_final: 0.8477 (p0) REVERT: E 439 ARG cc_start: 0.8712 (tmm-80) cc_final: 0.8394 (tmm-80) REVERT: F 200 GLN cc_start: 0.8905 (mm110) cc_final: 0.8396 (mp10) REVERT: F 213 MET cc_start: 0.4654 (ttp) cc_final: 0.1174 (tpt) REVERT: F 228 VAL cc_start: 0.8796 (t) cc_final: 0.8560 (t) REVERT: F 245 GLN cc_start: 0.8819 (pt0) cc_final: 0.8515 (mm-40) REVERT: F 307 ASP cc_start: 0.8860 (m-30) cc_final: 0.8637 (t0) REVERT: F 339 GLU cc_start: 0.8519 (pm20) cc_final: 0.8072 (pm20) outliers start: 25 outliers final: 14 residues processed: 204 average time/residue: 0.1616 time to fit residues: 44.3984 Evaluate side-chains 186 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 438 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 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 = 0.3579 r_free = 0.3579 target = 0.056805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046386 restraints weight = 93558.908| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.14 r_work: 0.3040 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13963 Z= 0.229 Angle : 0.743 10.600 18907 Z= 0.379 Chirality : 0.047 0.269 2099 Planarity : 0.005 0.053 2409 Dihedral : 6.901 84.637 2068 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 2.10 % Allowed : 19.53 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1652 helix: 2.70 (0.27), residues: 301 sheet: 0.05 (0.24), residues: 463 loop : -1.67 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.023 0.002 TYR E 64 PHE 0.030 0.002 PHE A 252 TRP 0.016 0.002 TRP A 351 HIS 0.007 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (13945) covalent geometry : angle 0.73458 / 0.38 (18861) SS BOND : bond 0.00855 / 0.41 ( 8) SS BOND : angle 1.42896 / 0.78 ( 16) hydrogen bonds : bond 0.06977 / 4.63 ( 527) hydrogen bonds : angle 5.21597 / 3.58 ( 1443) link_BETA1-4 : bond 0.00961 / 0.48 ( 3) link_BETA1-4 : angle 3.68311 / 2.46 ( 9) link_NAG-ASN : bond 0.00497 / 0.22 ( 7) link_NAG-ASN : angle 2.10274 / 1.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: A 105 TYR cc_start: 0.8892 (p90) cc_final: 0.8417 (p90) REVERT: A 142 TRP cc_start: 0.6588 (m100) cc_final: 0.6322 (m100) REVERT: A 257 ARG cc_start: 0.8482 (ptp-170) cc_final: 0.8242 (ptt-90) REVERT: B 37 LYS cc_start: 0.8963 (ttpt) cc_final: 0.8724 (ttpt) REVERT: B 261 MET cc_start: 0.8059 (tmm) cc_final: 0.7859 (tmm) REVERT: B 266 TYR cc_start: 0.8372 (m-80) cc_final: 0.8035 (m-80) REVERT: E 109 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9218 (mm) REVERT: E 249 LYS cc_start: 0.8940 (ptpt) cc_final: 0.8738 (ptpp) REVERT: E 307 ASP cc_start: 0.8632 (t0) cc_final: 0.8310 (t0) REVERT: E 366 ASN cc_start: 0.8857 (p0) cc_final: 0.8537 (p0) REVERT: E 439 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8454 (tmm-80) REVERT: F 213 MET cc_start: 0.5046 (ttp) cc_final: 0.1287 (tpt) REVERT: F 245 GLN cc_start: 0.8860 (pt0) cc_final: 0.8635 (mm-40) REVERT: F 273 ARG cc_start: 0.8513 (tpp80) cc_final: 0.8253 (tpp80) REVERT: F 339 GLU cc_start: 0.8529 (pm20) cc_final: 0.8149 (pm20) outliers start: 31 outliers final: 14 residues processed: 199 average time/residue: 0.1552 time to fit residues: 42.2842 Evaluate side-chains 182 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 375 CYS Chi-restraints excluded: chain F residue 438 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 154 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 200 GLN ** F 399 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 = 0.3604 r_free = 0.3604 target = 0.057741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047322 restraints weight = 92497.491| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.10 r_work: 0.3216 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13963 Z= 0.150 Angle : 0.707 10.720 18907 Z= 0.357 Chirality : 0.046 0.274 2099 Planarity : 0.005 0.052 2409 Dihedral : 6.636 85.873 2068 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 2.44 % Allowed : 19.73 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1652 helix: 2.94 (0.27), residues: 301 sheet: 0.06 (0.24), residues: 461 loop : -1.64 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.034 0.002 TYR E 64 PHE 0.027 0.002 PHE A 252 TRP 0.014 0.002 TRP A 351 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (13945) covalent geometry : angle 0.69925 / 0.35 (18861) SS BOND : bond 0.00908 / 0.46 ( 8) SS BOND : angle 1.35271 / 0.76 ( 16) hydrogen bonds : bond 0.06492 / 4.31 ( 527) hydrogen bonds : angle 5.08520 / 3.48 ( 1443) link_BETA1-4 : bond 0.01135 / 0.57 ( 3) link_BETA1-4 : angle 3.77001 / 2.49 ( 9) link_NAG-ASN : bond 0.00265 / 0.12 ( 7) link_NAG-ASN : angle 1.86216 / 1.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8896 (p90) cc_final: 0.8432 (p90) REVERT: A 142 TRP cc_start: 0.6190 (m100) cc_final: 0.5908 (m100) REVERT: A 257 ARG cc_start: 0.8527 (ptp-170) cc_final: 0.8245 (ptt-90) REVERT: B 181 MET cc_start: 0.9145 (ttm) cc_final: 0.8836 (tmm) REVERT: B 266 TYR cc_start: 0.8314 (m-80) cc_final: 0.7965 (m-80) REVERT: E 307 ASP cc_start: 0.8659 (t0) cc_final: 0.8415 (p0) REVERT: E 366 ASN cc_start: 0.8569 (p0) cc_final: 0.8240 (p0) REVERT: E 439 ARG cc_start: 0.8723 (tmm-80) cc_final: 0.8414 (tmm-80) REVERT: F 200 GLN cc_start: 0.8901 (mm110) cc_final: 0.8280 (mp10) REVERT: F 213 MET cc_start: 0.4313 (ttp) cc_final: 0.1035 (tpt) REVERT: F 245 GLN cc_start: 0.8776 (pt0) cc_final: 0.8451 (pt0) REVERT: F 339 GLU cc_start: 0.8248 (pm20) cc_final: 0.8043 (pm20) outliers start: 36 outliers final: 17 residues processed: 204 average time/residue: 0.1498 time to fit residues: 41.8379 Evaluate side-chains 191 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 375 CYS Chi-restraints excluded: chain F residue 438 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS A 410 ASN ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.057266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.046806 restraints weight = 92232.897| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.10 r_work: 0.3178 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13963 Z= 0.175 Angle : 0.738 12.531 18907 Z= 0.371 Chirality : 0.046 0.275 2099 Planarity : 0.005 0.057 2409 Dihedral : 6.623 86.652 2068 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 2.24 % Allowed : 20.27 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1652 helix: 2.89 (0.27), residues: 301 sheet: 0.05 (0.24), residues: 467 loop : -1.65 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.025 0.002 TYR E 64 PHE 0.018 0.002 PHE A 252 TRP 0.014 0.002 TRP A 351 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (13945) covalent geometry : angle 0.73010 / 0.37 (18861) SS BOND : bond 0.00662 / 0.31 ( 8) SS BOND : angle 1.40413 / 1.01 ( 16) hydrogen bonds : bond 0.06677 / 4.42 ( 527) hydrogen bonds : angle 5.12080 / 3.52 ( 1443) link_BETA1-4 : bond 0.01063 / 0.53 ( 3) link_BETA1-4 : angle 3.77468 / 2.52 ( 9) link_NAG-ASN : bond 0.00314 / 0.15 ( 7) link_NAG-ASN : angle 1.87272 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7614 (mp10) REVERT: A 105 TYR cc_start: 0.8836 (p90) cc_final: 0.8344 (p90) REVERT: A 142 TRP cc_start: 0.6349 (m100) cc_final: 0.6090 (m100) REVERT: A 152 ASN cc_start: 0.8283 (t0) cc_final: 0.8038 (t0) REVERT: A 474 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8990 (tp) REVERT: B 37 LYS cc_start: 0.8843 (pttp) cc_final: 0.8642 (tmmt) REVERT: B 104 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7326 (t80) REVERT: B 266 TYR cc_start: 0.8362 (m-80) cc_final: 0.8036 (m-80) REVERT: E 307 ASP cc_start: 0.8649 (t0) cc_final: 0.8437 (p0) REVERT: E 366 ASN cc_start: 0.8706 (p0) cc_final: 0.8423 (p0) REVERT: E 439 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8377 (tmm-80) REVERT: F 22 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6770 (ttp80) REVERT: F 200 GLN cc_start: 0.8858 (mm110) cc_final: 0.8275 (mp10) REVERT: F 213 MET cc_start: 0.4216 (ttp) cc_final: 0.0965 (tpt) REVERT: F 245 GLN cc_start: 0.8779 (pt0) cc_final: 0.8514 (pt0) REVERT: F 359 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7073 (t80) outliers start: 33 outliers final: 21 residues processed: 207 average time/residue: 0.1444 time to fit residues: 41.2862 Evaluate side-chains 197 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 359 TYR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 375 CYS Chi-restraints excluded: chain F residue 438 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 145 optimal weight: 0.0040 chunk 7 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** F 399 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 = 0.3614 r_free = 0.3614 target = 0.058082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047695 restraints weight = 91714.398| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.10 r_work: 0.3169 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13963 Z= 0.141 Angle : 0.754 15.026 18907 Z= 0.374 Chirality : 0.046 0.277 2099 Planarity : 0.005 0.060 2409 Dihedral : 6.425 84.920 2068 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 1.83 % Allowed : 21.76 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1652 helix: 2.93 (0.27), residues: 301 sheet: 0.09 (0.24), residues: 461 loop : -1.63 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 182 TYR 0.051 0.002 TYR E 64 PHE 0.026 0.001 PHE A 240 TRP 0.012 0.001 TRP A 351 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (13945) covalent geometry : angle 0.74724 / 0.37 (18861) SS BOND : bond 0.00726 / 0.36 ( 8) SS BOND : angle 1.26747 / 0.73 ( 16) hydrogen bonds : bond 0.06361 / 4.21 ( 527) hydrogen bonds : angle 5.03318 / 3.44 ( 1443) link_BETA1-4 : bond 0.01160 / 0.58 ( 3) link_BETA1-4 : angle 3.83082 / 2.54 ( 9) link_NAG-ASN : bond 0.00226 / 0.11 ( 7) link_NAG-ASN : angle 1.81051 / 1.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: A 105 TYR cc_start: 0.8785 (p90) cc_final: 0.8301 (p90) REVERT: A 138 ARG cc_start: 0.8066 (ttm110) cc_final: 0.6702 (mtt90) REVERT: A 142 TRP cc_start: 0.6213 (m100) cc_final: 0.5985 (m100) REVERT: A 234 LEU cc_start: 0.8587 (mt) cc_final: 0.8384 (pp) REVERT: A 246 GLU cc_start: 0.8812 (mp0) cc_final: 0.8518 (mp0) REVERT: A 257 ARG cc_start: 0.8261 (ptp90) cc_final: 0.7900 (ptt-90) REVERT: A 404 MET cc_start: 0.8648 (ttp) cc_final: 0.8386 (ttp) REVERT: B 104 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7335 (t80) REVERT: B 266 TYR cc_start: 0.8323 (m-80) cc_final: 0.7958 (m-80) REVERT: E 366 ASN cc_start: 0.8723 (p0) cc_final: 0.8440 (p0) REVERT: E 439 ARG cc_start: 0.8716 (tmm-80) cc_final: 0.8387 (tmm-80) REVERT: F 22 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6692 (ttp80) REVERT: F 200 GLN cc_start: 0.8870 (mm110) cc_final: 0.8346 (mp10) REVERT: F 213 MET cc_start: 0.4470 (ttp) cc_final: 0.1146 (tpt) outliers start: 27 outliers final: 19 residues processed: 199 average time/residue: 0.1599 time to fit residues: 43.0638 Evaluate side-chains 192 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 375 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 HIS ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 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 = 0.3586 r_free = 0.3586 target = 0.057019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.046602 restraints weight = 93089.496| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.12 r_work: 0.3167 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13963 Z= 0.187 Angle : 0.789 14.835 18907 Z= 0.396 Chirality : 0.047 0.278 2099 Planarity : 0.005 0.060 2409 Dihedral : 6.544 86.820 2068 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 1.90 % Allowed : 22.51 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1652 helix: 2.76 (0.27), residues: 301 sheet: 0.08 (0.24), residues: 471 loop : -1.65 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 187 TYR 0.055 0.002 TYR E 64 PHE 0.015 0.002 PHE A 240 TRP 0.028 0.002 TRP A 150 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (13945) covalent geometry : angle 0.78212 / 0.39 (18861) SS BOND : bond 0.00734 / 0.34 ( 8) SS BOND : angle 1.41319 / 1.02 ( 16) hydrogen bonds : bond 0.06725 / 4.44 ( 527) hydrogen bonds : angle 5.11962 / 3.52 ( 1443) link_BETA1-4 : bond 0.00899 / 0.45 ( 3) link_BETA1-4 : angle 3.76153 / 2.55 ( 9) link_NAG-ASN : bond 0.00340 / 0.17 ( 7) link_NAG-ASN : angle 1.87656 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: A 105 TYR cc_start: 0.8817 (p90) cc_final: 0.8338 (p90) REVERT: A 142 TRP cc_start: 0.6378 (m100) cc_final: 0.6053 (m100) REVERT: A 246 GLU cc_start: 0.8848 (mp0) cc_final: 0.8595 (mp0) REVERT: A 252 PHE cc_start: 0.8978 (p90) cc_final: 0.8635 (p90) REVERT: A 474 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9004 (tp) REVERT: B 104 PHE cc_start: 0.7927 (t80) cc_final: 0.7506 (t80) REVERT: B 266 TYR cc_start: 0.8365 (m-80) cc_final: 0.8037 (m-80) REVERT: E 366 ASN cc_start: 0.8756 (p0) cc_final: 0.8479 (p0) REVERT: E 439 ARG cc_start: 0.8691 (tmm-80) cc_final: 0.8372 (tmm-80) REVERT: F 22 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6871 (ttp80) REVERT: F 200 GLN cc_start: 0.8902 (mm110) cc_final: 0.8349 (mp10) REVERT: F 213 MET cc_start: 0.4377 (ttp) cc_final: 0.1064 (tpt) REVERT: F 245 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: F 359 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7423 (t80) REVERT: F 438 MET cc_start: 0.8461 (mmm) cc_final: 0.8115 (mtp) outliers start: 28 outliers final: 22 residues processed: 196 average time/residue: 0.1459 time to fit residues: 39.5254 Evaluate side-chains 199 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 411 ARG Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 359 TYR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 375 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 161 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 HIS ** F 399 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 = 0.3593 r_free = 0.3593 target = 0.057187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046802 restraints weight = 92221.167| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 4.10 r_work: 0.3178 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13963 Z= 0.165 Angle : 0.804 15.392 18907 Z= 0.401 Chirality : 0.047 0.286 2099 Planarity : 0.005 0.061 2409 Dihedral : 6.525 87.614 2068 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 2.03 % Allowed : 22.78 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1652 helix: 2.81 (0.27), residues: 301 sheet: 0.05 (0.24), residues: 466 loop : -1.65 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 404 TYR 0.057 0.002 TYR E 64 PHE 0.020 0.002 PHE B 99 TRP 0.025 0.002 TRP A 150 HIS 0.010 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (13945) covalent geometry : angle 0.79659 / 0.40 (18861) SS BOND : bond 0.00658 / 0.31 ( 8) SS BOND : angle 1.61408 / 0.95 ( 16) hydrogen bonds : bond 0.06662 / 4.41 ( 527) hydrogen bonds : angle 5.16114 / 3.53 ( 1443) link_BETA1-4 : bond 0.01054 / 0.53 ( 3) link_BETA1-4 : angle 3.80951 / 2.53 ( 9) link_NAG-ASN : bond 0.00274 / 0.13 ( 7) link_NAG-ASN : angle 1.87127 / 1.15 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: A 105 TYR cc_start: 0.8864 (p90) cc_final: 0.8376 (p90) REVERT: A 142 TRP cc_start: 0.6276 (m100) cc_final: 0.5970 (m100) REVERT: B 104 PHE cc_start: 0.7891 (t80) cc_final: 0.7478 (t80) REVERT: B 181 MET cc_start: 0.8960 (tmm) cc_final: 0.8607 (tmm) REVERT: B 266 TYR cc_start: 0.8396 (m-80) cc_final: 0.8036 (m-80) REVERT: E 366 ASN cc_start: 0.8673 (p0) cc_final: 0.8392 (p0) REVERT: E 439 ARG cc_start: 0.8673 (tmm-80) cc_final: 0.8350 (tmm-80) REVERT: F 22 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6878 (ttp80) REVERT: F 137 CYS cc_start: 0.5255 (p) cc_final: 0.5026 (p) REVERT: F 200 GLN cc_start: 0.8949 (mm110) cc_final: 0.8414 (mp10) REVERT: F 213 MET cc_start: 0.4276 (ttp) cc_final: 0.1054 (tpt) REVERT: F 359 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7410 (t80) REVERT: F 438 MET cc_start: 0.8462 (mmm) cc_final: 0.8101 (mtp) outliers start: 30 outliers final: 23 residues processed: 194 average time/residue: 0.1438 time to fit residues: 38.2686 Evaluate side-chains 198 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 411 ARG Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 359 TYR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 375 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 80 optimal weight: 0.0970 chunk 115 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 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 = 0.3564 r_free = 0.3564 target = 0.056145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.045850 restraints weight = 92549.555| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.05 r_work: 0.3032 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13963 Z= 0.210 Angle : 0.832 15.044 18907 Z= 0.417 Chirality : 0.048 0.289 2099 Planarity : 0.005 0.064 2409 Dihedral : 6.699 88.831 2068 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 1.90 % Allowed : 22.71 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1652 helix: 2.53 (0.27), residues: 301 sheet: -0.05 (0.24), residues: 462 loop : -1.65 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 257 TYR 0.022 0.002 TYR F 359 PHE 0.038 0.002 PHE E 257 TRP 0.027 0.002 TRP A 150 HIS 0.014 0.002 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (13945) covalent geometry : angle 0.82484 / 0.42 (18861) SS BOND : bond 0.00884 / 0.41 ( 8) SS BOND : angle 1.56790 / 0.90 ( 16) hydrogen bonds : bond 0.07137 / 4.71 ( 527) hydrogen bonds : angle 5.31518 / 3.65 ( 1443) link_BETA1-4 : bond 0.00919 / 0.46 ( 3) link_BETA1-4 : angle 3.82080 / 2.56 ( 9) link_NAG-ASN : bond 0.00431 / 0.22 ( 7) link_NAG-ASN : angle 1.96721 / 1.23 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4254.64 seconds wall clock time: 73 minutes 33.57 seconds (4413.57 seconds total)