Starting phenix.real_space_refine on Fri Jul 3 17:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrd_34053/07_2026/7yrd_34053.cif" } resolution = 3.2 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= 0.032 sd= 1.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1830 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 32 5.16 5 C 8067 2.51 5 N 2643 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14276 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 791 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 790 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 841 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 837 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 2056 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 2082 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13646 SG CYS K 275 34.989 21.023 55.188 1.00 81.78 S ATOM 13990 SG CYS K 319 32.495 18.444 53.871 1.00 86.30 S ATOM 14005 SG CYS K 321 36.070 17.784 53.089 1.00 93.18 S ATOM 14030 SG CYS K 324 34.891 17.744 56.692 1.00 91.95 S Time building chain proxies: 4.03, per 1000 atoms: 0.28 Number of scatterers: 14276 At special positions: 0 Unit cell: (116, 101, 114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 290 15.00 O 3243 8.00 N 2643 7.00 C 8067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K 279 " - pdb=" SG CYS K 305 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 521.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 324 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 275 " Number of angles added : 6 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 61.5% alpha, 4.9% beta 136 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.677A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.534A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.613A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 77 removed outlier: 3.593A pdb=" N VAL C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.776A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.640A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.522A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 76 removed outlier: 3.595A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 removed outlier: 3.579A pdb=" N ASP G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.700A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.561A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 73 through 94 removed outlier: 4.146A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Proline residue: K 91 - end of helix Processing helix chain 'K' and resid 134 through 148 removed outlier: 3.876A pdb=" N LYS K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 160 through 167 removed outlier: 3.668A pdb=" N ARG K 164 " --> pdb=" O GLY K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 187 removed outlier: 3.546A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG K 187 " --> pdb=" O PHE K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 243 Processing helix chain 'K' and resid 266 through 271 removed outlier: 3.587A pdb=" N ILE K 271 " --> pdb=" O ALA K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 326 Processing helix chain 'K' and resid 354 through 363 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.001A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 46 removed outlier: 6.736A pdb=" N ARG C 45 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.915A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 45 through 46 removed outlier: 7.413A pdb=" N ARG G 45 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AB1, first strand: chain 'K' and resid 195 through 199 Processing sheet with id=AB2, first strand: chain 'K' and resid 261 through 265 removed outlier: 3.552A pdb=" N ASP K 222 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL K 291 " --> pdb=" O ILE K 224 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N LEU K 226 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 12.158A pdb=" N ALA K 289 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 292 " --> pdb=" O LYS K 280 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS K 280 " --> pdb=" O LYS K 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 272 through 273 removed outlier: 6.242A pdb=" N ASN K 272 " --> pdb=" O CYS K 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 471 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1624 1.29 - 1.42: 5138 1.42 - 1.55: 7726 1.55 - 1.68: 587 1.68 - 1.81: 51 Bond restraints: 15126 Sorted by residual: bond pdb=" N ARG K 357 " pdb=" CA ARG K 357 " ideal model delta sigma weight residual 1.459 1.344 0.115 1.23e-02 6.61e+03 8.71e+01 bond pdb=" CA LYS K 362 " pdb=" C LYS K 362 " ideal model delta sigma weight residual 1.524 1.638 -0.115 1.27e-02 6.20e+03 8.14e+01 bond pdb=" CA LEU K 358 " pdb=" C LEU K 358 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.35e-02 5.49e+03 6.03e+01 bond pdb=" N THR K 354 " pdb=" CA THR K 354 " ideal model delta sigma weight residual 1.457 1.364 0.093 1.29e-02 6.01e+03 5.25e+01 bond pdb=" CA VAL B 21 " pdb=" C VAL B 21 " ideal model delta sigma weight residual 1.525 1.377 0.148 2.10e-02 2.27e+03 4.95e+01 ... (remaining 15121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 21055 2.33 - 4.66: 532 4.66 - 6.99: 44 6.99 - 9.32: 15 9.32 - 11.65: 3 Bond angle restraints: 21649 Sorted by residual: angle pdb=" C LEU K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" N LYS K 356 " pdb=" CA LYS K 356 " pdb=" C LYS K 356 " ideal model delta sigma weight residual 111.14 118.01 -6.87 1.08e+00 8.57e-01 4.05e+01 angle pdb=" N GLY B 9 " pdb=" CA GLY B 9 " pdb=" C GLY B 9 " ideal model delta sigma weight residual 112.49 119.23 -6.74 1.21e+00 6.83e-01 3.10e+01 angle pdb=" N ASN K 359 " pdb=" CA ASN K 359 " pdb=" C ASN K 359 " ideal model delta sigma weight residual 111.36 105.43 5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" CA ARG K 357 " pdb=" C ARG K 357 " pdb=" N LEU K 358 " ideal model delta sigma weight residual 117.39 123.54 -6.15 1.24e+00 6.50e-01 2.46e+01 ... (remaining 21644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 6740 31.24 - 62.49: 1615 62.49 - 93.73: 59 93.73 - 124.98: 1 124.98 - 156.22: 4 Dihedral angle restraints: 8419 sinusoidal: 5387 harmonic: 3032 Sorted by residual: dihedral pdb=" CB CYS K 279 " pdb=" SG CYS K 279 " pdb=" SG CYS K 305 " pdb=" CB CYS K 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.86 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" C ECX B 20 " pdb=" N ECX B 20 " pdb=" CA ECX B 20 " pdb=" CB ECX B 20 " ideal model delta harmonic sigma weight residual -122.60 -108.07 -14.53 0 2.50e+00 1.60e-01 3.38e+01 dihedral pdb=" CA GLY B 11 " pdb=" C GLY B 11 " pdb=" N LYS B 12 " pdb=" CA LYS B 12 " ideal model delta harmonic sigma weight residual -180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 8416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2332 0.103 - 0.207: 101 0.207 - 0.310: 2 0.310 - 0.414: 1 0.414 - 0.517: 2 Chirality restraints: 2438 Sorted by residual: chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CB VAL B 21 " pdb=" CA VAL B 21 " pdb=" CG1 VAL B 21 " pdb=" CG2 VAL B 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA LEU K 358 " pdb=" N LEU K 358 " pdb=" C LEU K 358 " pdb=" CB LEU K 358 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 2435 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 362 " 0.025 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C LYS K 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS K 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS K 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 21 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C VAL B 21 " 0.069 2.00e-02 2.50e+03 pdb=" O VAL B 21 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 22 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 359 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ASN K 359 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN K 359 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG K 360 " 0.021 2.00e-02 2.50e+03 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 205 2.63 - 3.19: 11835 3.19 - 3.76: 25843 3.76 - 4.33: 34557 4.33 - 4.90: 50019 Nonbonded interactions: 122459 Sorted by model distance: nonbonded pdb=" CG2 VAL B 21 " pdb=" C MET K 253 " model vdw 2.057 3.690 nonbonded pdb=" O LEU C 117 " pdb=" NZ LYS F 44 " model vdw 2.088 3.120 nonbonded pdb=" OH TYR K 254 " pdb=" OD1 ASN K 259 " model vdw 2.097 3.040 nonbonded pdb=" O LYS C 37 " pdb=" OG1 THR C 40 " model vdw 2.130 3.040 nonbonded pdb=" CD ARG K 295 " pdb=" OD2 ASP K 355 " model vdw 2.131 3.440 ... (remaining 122454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 36 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'C' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 118)) selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.480 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.008 0.286 15132 Z= 0.638 Angle : 0.875 11.650 21657 Z= 0.719 Chirality : 0.050 0.517 2438 Planarity : 0.005 0.073 1733 Dihedral : 26.758 156.219 6464 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.70 % Allowed : 1.04 % Favored : 98.26 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.25), residues: 1027 helix: 0.50 (0.20), residues: 637 sheet: -1.44 (0.68), residues: 40 loop : -2.14 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 357 TYR 0.012 0.002 TYR G 60 PHE 0.013 0.002 PHE K 154 TRP 0.007 0.001 TRP K 264 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.59 (15126) covalent geometry : angle 0.87124 / 0.72 (21649) SS BOND : bond 0.00286 / 0.15 ( 1) SS BOND : angle 0.82369 / 0.48 ( 2) hydrogen bonds : bond 0.12104 / 7.91 ( 799) hydrogen bonds : angle 4.97473 / 3.52 ( 2045) metal coordination : bond 0.01063 / 0.52 ( 4) metal coordination : angle 5.08305 / 1.90 ( 6) Misc. bond : bond 0.28575 / 15.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.398 Fit side-chains REVERT: B 92 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8156 (mtp-110) REVERT: H 120 LYS cc_start: 0.7853 (ttmt) cc_final: 0.6958 (tptt) REVERT: K 219 LYS cc_start: 0.7589 (mmmm) cc_final: 0.7037 (mmmm) REVERT: K 276 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7034 (tmt170) REVERT: K 312 PHE cc_start: 0.7504 (m-10) cc_final: 0.7255 (m-10) outliers start: 4 outliers final: 0 residues processed: 247 average time/residue: 0.1719 time to fit residues: 56.6856 Evaluate side-chains 230 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 109 HIS K 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.190992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131447 restraints weight = 23784.293| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.10 r_work: 0.3083 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15132 Z= 0.185 Angle : 0.771 9.670 21657 Z= 0.440 Chirality : 0.053 0.271 2438 Planarity : 0.006 0.054 1733 Dihedral : 30.202 152.346 4437 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 1.16 % Allowed : 9.16 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.25), residues: 1027 helix: 0.80 (0.20), residues: 644 sheet: -1.33 (0.68), residues: 40 loop : -2.15 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 357 TYR 0.016 0.002 TYR K 254 PHE 0.012 0.001 PHE K 178 TRP 0.002 0.001 TRP K 264 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (15126) covalent geometry : angle 0.76633 / 0.44 (21649) SS BOND : bond 0.00031 / 0.02 ( 1) SS BOND : angle 1.68363 / 0.99 ( 2) hydrogen bonds : bond 0.07189 / 4.79 ( 799) hydrogen bonds : angle 4.03398 / 2.89 ( 2045) metal coordination : bond 0.00912 / 0.45 ( 4) metal coordination : angle 4.79316 / 1.89 ( 6) Misc. bond : bond 0.00226 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 238 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 ARG cc_start: 0.9180 (tpt170) cc_final: 0.8959 (tpt170) REVERT: D 47 GLN cc_start: 0.8014 (tp40) cc_final: 0.7797 (tp40) REVERT: E 73 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8718 (tm-30) REVERT: G 34 ARG cc_start: 0.8943 (ttp80) cc_final: 0.8723 (ttp80) REVERT: G 75 ASP cc_start: 0.7567 (m-30) cc_final: 0.7359 (m-30) REVERT: H 120 LYS cc_start: 0.7896 (ttmt) cc_final: 0.6782 (tptt) REVERT: K 219 LYS cc_start: 0.7204 (mmmm) cc_final: 0.6668 (mmmm) REVERT: K 348 LYS cc_start: 0.7340 (mtmm) cc_final: 0.7105 (ptpp) outliers start: 8 outliers final: 6 residues processed: 240 average time/residue: 0.1752 time to fit residues: 56.0797 Evaluate side-chains 236 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN H 109 HIS K 181 HIS K 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.190007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130452 restraints weight = 17150.356| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.81 r_work: 0.3129 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 15132 Z= 0.223 Angle : 0.735 9.021 21657 Z= 0.425 Chirality : 0.049 0.270 2438 Planarity : 0.006 0.111 1733 Dihedral : 30.236 151.616 4437 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.74 % Allowed : 11.37 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1027 helix: 0.86 (0.20), residues: 645 sheet: -1.20 (0.80), residues: 26 loop : -2.11 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 49 TYR 0.019 0.002 TYR K 254 PHE 0.012 0.002 PHE K 154 TRP 0.008 0.001 TRP K 264 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (15126) covalent geometry : angle 0.73108 / 0.42 (21649) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 1.53632 / 0.90 ( 2) hydrogen bonds : bond 0.06984 / 4.64 ( 799) hydrogen bonds : angle 3.95785 / 2.82 ( 2045) metal coordination : bond 0.00879 / 0.43 ( 4) metal coordination : angle 4.48427 / 1.84 ( 6) Misc. bond : bond 0.00479 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8426 (pm20) cc_final: 0.8218 (pm20) REVERT: A 134 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: D 47 GLN cc_start: 0.8007 (tp40) cc_final: 0.7728 (tp40) REVERT: E 73 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8677 (tm-30) REVERT: G 34 ARG cc_start: 0.8929 (ttp80) cc_final: 0.8709 (ttp80) REVERT: G 75 ASP cc_start: 0.7641 (m-30) cc_final: 0.7399 (m-30) REVERT: K 72 MET cc_start: 0.7305 (pmm) cc_final: 0.6957 (pmm) REVERT: K 219 LYS cc_start: 0.7253 (mmmm) cc_final: 0.6709 (mmmm) REVERT: K 332 PHE cc_start: 0.5695 (m-80) cc_final: 0.4642 (m-80) REVERT: K 353 GLU cc_start: 0.7197 (tp30) cc_final: 0.6962 (tp30) outliers start: 13 outliers final: 11 residues processed: 233 average time/residue: 0.1625 time to fit residues: 50.9817 Evaluate side-chains 236 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.191898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.133147 restraints weight = 23893.766| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.06 r_work: 0.3100 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15132 Z= 0.161 Angle : 0.676 7.901 21657 Z= 0.400 Chirality : 0.048 0.271 2438 Planarity : 0.005 0.065 1733 Dihedral : 30.196 152.121 4437 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.62 % Allowed : 12.76 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1027 helix: 0.99 (0.20), residues: 645 sheet: -1.26 (0.81), residues: 26 loop : -2.05 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 3 TYR 0.023 0.001 TYR F 88 PHE 0.012 0.001 PHE K 281 TRP 0.003 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (15126) covalent geometry : angle 0.67146 / 0.40 (21649) SS BOND : bond 0.00221 / 0.12 ( 1) SS BOND : angle 1.71359 / 1.01 ( 2) hydrogen bonds : bond 0.06139 / 4.11 ( 799) hydrogen bonds : angle 3.74155 / 2.68 ( 2045) metal coordination : bond 0.00764 / 0.37 ( 4) metal coordination : angle 4.48526 / 1.87 ( 6) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 GLN cc_start: 0.8117 (tp40) cc_final: 0.7839 (tp40) REVERT: E 73 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8747 (tm-30) REVERT: G 34 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8739 (ttp80) REVERT: G 75 ASP cc_start: 0.7642 (m-30) cc_final: 0.7394 (m-30) REVERT: K 72 MET cc_start: 0.7223 (pmm) cc_final: 0.6924 (pmm) REVERT: K 332 PHE cc_start: 0.5593 (m-80) cc_final: 0.4532 (m-80) REVERT: K 353 GLU cc_start: 0.7244 (tp30) cc_final: 0.7031 (tp30) outliers start: 12 outliers final: 6 residues processed: 236 average time/residue: 0.1630 time to fit residues: 51.8580 Evaluate side-chains 230 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 348 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.193381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.133701 restraints weight = 20897.459| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.94 r_work: 0.3158 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15132 Z= 0.146 Angle : 0.658 8.872 21657 Z= 0.387 Chirality : 0.047 0.278 2438 Planarity : 0.005 0.058 1733 Dihedral : 30.176 154.301 4437 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.74 % Allowed : 13.57 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1027 helix: 1.25 (0.20), residues: 644 sheet: -1.34 (0.69), residues: 40 loop : -2.05 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 326 TYR 0.028 0.001 TYR F 88 PHE 0.013 0.001 PHE K 311 TRP 0.008 0.002 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (15126) covalent geometry : angle 0.65531 / 0.39 (21649) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 1.66633 / 0.98 ( 2) hydrogen bonds : bond 0.05589 / 3.75 ( 799) hydrogen bonds : angle 3.59676 / 2.57 ( 2045) metal coordination : bond 0.00589 / 0.29 ( 4) metal coordination : angle 3.73153 / 1.59 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8679 (mtt-85) REVERT: D 47 GLN cc_start: 0.8207 (tp40) cc_final: 0.7936 (tp40) REVERT: G 75 ASP cc_start: 0.7693 (m-30) cc_final: 0.7449 (m-30) REVERT: H 120 LYS cc_start: 0.7912 (tttt) cc_final: 0.6813 (tptt) REVERT: K 72 MET cc_start: 0.7295 (pmm) cc_final: 0.7051 (pmm) REVERT: K 332 PHE cc_start: 0.5528 (m-80) cc_final: 0.4474 (m-80) REVERT: K 348 LYS cc_start: 0.7556 (mtmm) cc_final: 0.7189 (ptpp) outliers start: 14 outliers final: 10 residues processed: 231 average time/residue: 0.1599 time to fit residues: 49.8822 Evaluate side-chains 228 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 85 optimal weight: 0.0470 chunk 114 optimal weight: 3.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.190616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132696 restraints weight = 29232.787| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.31 r_work: 0.3063 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15132 Z= 0.206 Angle : 0.684 8.069 21657 Z= 0.397 Chirality : 0.048 0.282 2438 Planarity : 0.005 0.063 1733 Dihedral : 30.298 157.260 4437 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.86 % Allowed : 13.92 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1027 helix: 1.06 (0.20), residues: 645 sheet: -1.34 (0.77), residues: 26 loop : -2.04 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 326 TYR 0.012 0.001 TYR G 60 PHE 0.010 0.001 PHE E 104 TRP 0.002 0.001 TRP K 264 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (15126) covalent geometry : angle 0.68011 / 0.40 (21649) SS BOND : bond 0.00199 / 0.10 ( 1) SS BOND : angle 1.46212 / 0.86 ( 2) hydrogen bonds : bond 0.06244 / 4.20 ( 799) hydrogen bonds : angle 3.70736 / 2.64 ( 2045) metal coordination : bond 0.00771 / 0.38 ( 4) metal coordination : angle 4.10232 / 1.73 ( 6) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8923 (mtt-85) cc_final: 0.8704 (mtt-85) REVERT: D 47 GLN cc_start: 0.8282 (tp40) cc_final: 0.8029 (tp40) REVERT: E 73 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8837 (tm-30) REVERT: K 72 MET cc_start: 0.7259 (pmm) cc_final: 0.6973 (pmm) REVERT: K 332 PHE cc_start: 0.5613 (m-80) cc_final: 0.4553 (m-80) REVERT: K 356 LYS cc_start: 0.5763 (tttt) cc_final: 0.5410 (ttpt) outliers start: 15 outliers final: 13 residues processed: 233 average time/residue: 0.1558 time to fit residues: 48.4875 Evaluate side-chains 238 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 39 optimal weight: 10.9990 chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.191325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.132587 restraints weight = 23897.004| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.05 r_work: 0.3087 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15132 Z= 0.186 Angle : 0.672 8.386 21657 Z= 0.391 Chirality : 0.048 0.283 2438 Planarity : 0.004 0.055 1733 Dihedral : 30.329 156.631 4437 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.20 % Allowed : 14.97 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1027 helix: 1.10 (0.20), residues: 645 sheet: -1.37 (0.78), residues: 26 loop : -2.01 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 286 TYR 0.010 0.001 TYR G 60 PHE 0.009 0.001 PHE K 311 TRP 0.004 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (15126) covalent geometry : angle 0.66849 / 0.39 (21649) SS BOND : bond 0.00121 / 0.06 ( 1) SS BOND : angle 1.48455 / 0.87 ( 2) hydrogen bonds : bond 0.06054 / 4.09 ( 799) hydrogen bonds : angle 3.66327 / 2.62 ( 2045) metal coordination : bond 0.00703 / 0.35 ( 4) metal coordination : angle 4.26222 / 1.78 ( 6) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8870 (mtt-85) cc_final: 0.8653 (mtt-85) REVERT: D 47 GLN cc_start: 0.8253 (tp40) cc_final: 0.7996 (tp40) REVERT: E 73 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8824 (tm-30) REVERT: K 72 MET cc_start: 0.7247 (pmm) cc_final: 0.6995 (pmm) REVERT: K 219 LYS cc_start: 0.7285 (mmmm) cc_final: 0.6702 (mmmm) REVERT: K 332 PHE cc_start: 0.5575 (m-80) cc_final: 0.4520 (m-80) outliers start: 18 outliers final: 17 residues processed: 236 average time/residue: 0.1546 time to fit residues: 49.0818 Evaluate side-chains 245 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 0.0040 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 30.0000 chunk 47 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 overall best weight: 2.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.189599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.130338 restraints weight = 20477.874| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.94 r_work: 0.3079 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15132 Z= 0.228 Angle : 0.700 8.119 21657 Z= 0.402 Chirality : 0.049 0.285 2438 Planarity : 0.005 0.049 1733 Dihedral : 30.406 157.067 4437 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.44 % Allowed : 15.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1027 helix: 0.95 (0.20), residues: 645 sheet: -1.44 (0.79), residues: 26 loop : -2.08 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 49 TYR 0.012 0.002 TYR G 60 PHE 0.011 0.002 PHE G 27 TRP 0.003 0.001 TRP K 264 HIS 0.006 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (15126) covalent geometry : angle 0.69564 / 0.40 (21649) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 1.59186 / 0.93 ( 2) hydrogen bonds : bond 0.06527 / 4.41 ( 799) hydrogen bonds : angle 3.74294 / 2.67 ( 2045) metal coordination : bond 0.00891 / 0.44 ( 4) metal coordination : angle 4.68827 / 1.91 ( 6) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8664 (mtt-85) REVERT: C 22 ARG cc_start: 0.8922 (ttm170) cc_final: 0.8691 (ttm170) REVERT: D 34 LYS cc_start: 0.7427 (ptpt) cc_final: 0.7049 (pttm) REVERT: D 47 GLN cc_start: 0.8156 (tp40) cc_final: 0.7864 (tp40) REVERT: E 73 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8806 (tm-30) REVERT: K 72 MET cc_start: 0.7263 (pmm) cc_final: 0.6995 (pmm) REVERT: K 332 PHE cc_start: 0.5654 (m-80) cc_final: 0.4589 (m-80) outliers start: 20 outliers final: 19 residues processed: 242 average time/residue: 0.1747 time to fit residues: 56.0134 Evaluate side-chains 249 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.192681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.131262 restraints weight = 17228.626| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.70 r_work: 0.3173 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15132 Z= 0.149 Angle : 0.649 8.832 21657 Z= 0.380 Chirality : 0.046 0.276 2438 Planarity : 0.004 0.055 1733 Dihedral : 30.335 156.405 4437 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.32 % Allowed : 16.24 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1027 helix: 1.23 (0.20), residues: 647 sheet: -1.30 (0.79), residues: 26 loop : -1.99 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 326 TYR 0.010 0.001 TYR E 54 PHE 0.010 0.001 PHE K 311 TRP 0.003 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (15126) covalent geometry : angle 0.64509 / 0.38 (21649) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 1.50529 / 0.88 ( 2) hydrogen bonds : bond 0.05664 / 3.85 ( 799) hydrogen bonds : angle 3.57342 / 2.56 ( 2045) metal coordination : bond 0.00637 / 0.31 ( 4) metal coordination : angle 4.32751 / 1.77 ( 6) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8381 (mp-120) REVERT: D 34 LYS cc_start: 0.7457 (ptpt) cc_final: 0.7099 (pttm) REVERT: D 47 GLN cc_start: 0.8214 (tp40) cc_final: 0.7907 (tp40) REVERT: D 62 MET cc_start: 0.9020 (tpp) cc_final: 0.8752 (mmp) REVERT: E 73 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8746 (tm-30) REVERT: K 332 PHE cc_start: 0.5614 (m-80) cc_final: 0.4516 (m-80) REVERT: K 348 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7193 (ptpp) outliers start: 19 outliers final: 14 residues processed: 243 average time/residue: 0.1712 time to fit residues: 55.5028 Evaluate side-chains 246 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN K 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.193815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.135808 restraints weight = 20627.265| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.94 r_work: 0.3153 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15132 Z= 0.140 Angle : 0.648 8.826 21657 Z= 0.378 Chirality : 0.046 0.279 2438 Planarity : 0.004 0.044 1733 Dihedral : 30.296 158.539 4437 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.62 % Allowed : 17.17 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1027 helix: 1.31 (0.20), residues: 646 sheet: -1.22 (0.81), residues: 26 loop : -1.96 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 49 TYR 0.010 0.001 TYR E 54 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (15126) covalent geometry : angle 0.64462 / 0.38 (21649) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 1.35507 / 0.79 ( 2) hydrogen bonds : bond 0.05512 / 3.74 ( 799) hydrogen bonds : angle 3.53188 / 2.52 ( 2045) metal coordination : bond 0.00553 / 0.27 ( 4) metal coordination : angle 3.96286 / 1.66 ( 6) Misc. bond : bond 0.00028 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8380 (mp-120) REVERT: D 34 LYS cc_start: 0.7426 (ptpt) cc_final: 0.7056 (pttm) REVERT: D 47 GLN cc_start: 0.8233 (tp40) cc_final: 0.7925 (tp40) REVERT: D 62 MET cc_start: 0.9047 (tpp) cc_final: 0.8789 (mmp) REVERT: E 73 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8765 (tm-30) REVERT: G 75 ASP cc_start: 0.7664 (m-30) cc_final: 0.7345 (m-30) REVERT: K 332 PHE cc_start: 0.5491 (m-80) cc_final: 0.4441 (m-80) REVERT: K 348 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7218 (ptpp) outliers start: 13 outliers final: 11 residues processed: 225 average time/residue: 0.1614 time to fit residues: 49.2887 Evaluate side-chains 238 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 80.0000 chunk 106 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.189207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130212 restraints weight = 19233.901| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.90 r_work: 0.3090 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15132 Z= 0.264 Angle : 0.726 8.738 21657 Z= 0.412 Chirality : 0.049 0.290 2438 Planarity : 0.005 0.052 1733 Dihedral : 30.432 159.884 4437 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.86 % Allowed : 16.71 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1027 helix: 0.92 (0.20), residues: 645 sheet: -1.28 (0.78), residues: 26 loop : -2.12 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.012 0.002 TYR F 51 PHE 0.013 0.002 PHE E 104 TRP 0.002 0.001 TRP K 264 HIS 0.007 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.26 (15126) covalent geometry : angle 0.72223 / 0.41 (21649) SS BOND : bond 0.00315 / 0.17 ( 1) SS BOND : angle 1.52280 / 0.89 ( 2) hydrogen bonds : bond 0.06699 / 4.50 ( 799) hydrogen bonds : angle 3.79781 / 2.71 ( 2045) metal coordination : bond 0.00951 / 0.47 ( 4) metal coordination : angle 4.38751 / 1.80 ( 6) Misc. bond : bond 0.00010 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.56 seconds wall clock time: 67 minutes 5.59 seconds (4025.59 seconds total)