Starting phenix.real_space_refine on Thu Aug 6 13:11:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yrd_34053/08_2026/7yrd_34053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrd_34053/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2026/7yrd_34053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2026/7yrd_34053.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2026/7yrd_34053.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2026/7yrd_34053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2026/7yrd_34053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2026/7yrd_34053.map" } 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-2.2rc3-6140/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: 3.96, 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: 1.26 Conformation dependent library (CDL) restraints added in 515.0 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: 2.07 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: 3.21 Time building geometry restraints manager: 1.71 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: 21048 2.33 - 4.66: 539 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.780 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- 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= 0.639 Angle : 0.881 11.650 21657 Z= 0.724 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 0.87655 / 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 : 0.386 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: 0.1713 time to fit residues: 56.5380 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 : 0.400 ------------------------------------------------------------------------------- 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 = 0.190988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.131335 restraints weight = 23806.649| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.10 r_work: 0.3084 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- 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 = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15132 Z= 0.188 Angle : 0.787 9.958 21657 Z= 0.446 Chirality : 0.053 0.288 2438 Planarity : 0.006 0.053 1733 Dihedral : 30.160 152.386 4437 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 1.28 % Allowed : 9.16 % Favored : 89.56 % 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: -0.38 (0.25), residues: 1027 helix: 0.79 (0.20), residues: 644 sheet: -1.34 (0.67), residues: 40 loop : -2.15 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 357 TYR 0.011 0.002 TYR G 60 PHE 0.012 0.001 PHE E 67 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 0.00361 / 0.19 (15126) covalent geometry : angle 0.78247 / 0.45 (21649) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 1.71321 / 1.00 ( 2) hydrogen bonds : bond 0.07251 / 4.83 ( 799) hydrogen bonds : angle 4.05156 / 2.90 ( 2045) metal coordination : bond 0.00903 / 0.45 ( 4) metal coordination : angle 4.78519 / 1.88 ( 6) Misc. bond : bond 0.00100 / 0.05 ( 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 248 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8965 (tttt) cc_final: 0.8731 (tttm) REVERT: C 84 ARG cc_start: 0.9179 (tpt170) cc_final: 0.8964 (tpt170) REVERT: D 47 GLN cc_start: 0.8019 (tp40) cc_final: 0.7801 (tp40) REVERT: E 73 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8726 (tm-30) REVERT: G 34 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8727 (ttp80) REVERT: G 75 ASP cc_start: 0.7586 (m-30) cc_final: 0.7376 (m-30) REVERT: K 219 LYS cc_start: 0.7166 (mmmm) cc_final: 0.6642 (mmmm) REVERT: K 348 LYS cc_start: 0.7315 (mtmm) cc_final: 0.7081 (ptpp) outliers start: 9 outliers final: 7 residues processed: 241 average time/residue: 0.1496 time to fit residues: 48.3058 Evaluate side-chains 240 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL 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: 1.9990 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: 6.9990 chunk 99 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 109 HIS K 181 HIS K 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.189543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129716 restraints weight = 17151.771| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.87 r_work: 0.3117 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15132 Z= 0.237 Angle : 0.750 9.403 21657 Z= 0.432 Chirality : 0.050 0.297 2438 Planarity : 0.006 0.102 1733 Dihedral : 30.193 151.958 4437 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.74 % Allowed : 11.48 % Favored : 86.77 % 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: -0.34 (0.25), residues: 1027 helix: 0.83 (0.20), residues: 645 sheet: -1.22 (0.80), residues: 26 loop : -2.13 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 49 TYR 0.022 0.002 TYR K 254 PHE 0.011 0.002 PHE K 154 TRP 0.007 0.001 TRP K 264 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 (15126) covalent geometry : angle 0.74648 / 0.43 (21649) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 1.54674 / 0.91 ( 2) hydrogen bonds : bond 0.07126 / 4.73 ( 799) hydrogen bonds : angle 3.99132 / 2.85 ( 2045) metal coordination : bond 0.00941 / 0.46 ( 4) metal coordination : angle 4.52053 / 1.84 ( 6) Misc. bond : bond 0.00317 / 0.17 ( 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 243 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7862 (mmm-85) cc_final: 0.7504 (mmm-85) REVERT: D 47 GLN cc_start: 0.8015 (tp40) cc_final: 0.7794 (tp40) REVERT: E 73 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8697 (tm-30) REVERT: G 34 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8727 (ttp80) REVERT: G 75 ASP cc_start: 0.7646 (m-30) cc_final: 0.7404 (m-30) REVERT: K 219 LYS cc_start: 0.7249 (mmmm) cc_final: 0.6700 (mmmm) REVERT: K 332 PHE cc_start: 0.5691 (m-80) cc_final: 0.4634 (m-80) outliers start: 13 outliers final: 12 residues processed: 232 average time/residue: 0.1404 time to fit residues: 44.2481 Evaluate side-chains 237 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 D residue 118 VAL 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: 2.9990 chunk 75 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.191128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.132613 restraints weight = 23879.894| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.09 r_work: 0.3091 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15132 Z= 0.179 Angle : 0.699 8.247 21657 Z= 0.406 Chirality : 0.048 0.288 2438 Planarity : 0.005 0.063 1733 Dihedral : 30.172 151.631 4437 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.86 % Allowed : 13.81 % Favored : 84.34 % 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: -0.17 (0.25), residues: 1027 helix: 0.97 (0.20), residues: 645 sheet: -1.31 (0.81), residues: 26 loop : -2.07 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 3 TYR 0.019 0.001 TYR F 88 PHE 0.011 0.001 PHE K 311 TRP 0.006 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (15126) covalent geometry : angle 0.69464 / 0.41 (21649) SS BOND : bond 0.00078 / 0.04 ( 1) SS BOND : angle 1.48177 / 0.87 ( 2) hydrogen bonds : bond 0.06280 / 4.21 ( 799) hydrogen bonds : angle 3.76216 / 2.69 ( 2045) metal coordination : bond 0.00617 / 0.30 ( 4) metal coordination : angle 4.87193 / 1.97 ( 6) Misc. bond : bond 0.00075 / 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 242 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: D 47 GLN cc_start: 0.8108 (tp40) cc_final: 0.7874 (tp40) REVERT: E 73 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8744 (tm-30) REVERT: G 34 ARG cc_start: 0.8973 (ttp80) cc_final: 0.8725 (ttp80) REVERT: G 75 ASP cc_start: 0.7679 (m-30) cc_final: 0.7394 (m-30) REVERT: K 332 PHE cc_start: 0.5648 (m-80) cc_final: 0.4579 (m-80) REVERT: K 348 LYS cc_start: 0.7595 (mtmm) cc_final: 0.7304 (ptpp) outliers start: 14 outliers final: 11 residues processed: 233 average time/residue: 0.1369 time to fit residues: 43.1845 Evaluate side-chains 234 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 116 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain F residue 82 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.191699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132440 restraints weight = 20867.498| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.91 r_work: 0.3117 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15132 Z= 0.164 Angle : 0.676 8.806 21657 Z= 0.393 Chirality : 0.048 0.290 2438 Planarity : 0.004 0.056 1733 Dihedral : 30.195 154.264 4437 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.09 % Allowed : 14.62 % Favored : 83.29 % 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: -0.03 (0.25), residues: 1027 helix: 1.10 (0.20), residues: 645 sheet: -1.36 (0.80), residues: 26 loop : -2.06 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 326 TYR 0.014 0.001 TYR F 88 PHE 0.011 0.001 PHE K 311 TRP 0.006 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (15126) covalent geometry : angle 0.67256 / 0.39 (21649) SS BOND : bond 0.00177 / 0.09 ( 1) SS BOND : angle 1.49049 / 0.88 ( 2) hydrogen bonds : bond 0.05889 / 3.95 ( 799) hydrogen bonds : angle 3.65955 / 2.62 ( 2045) metal coordination : bond 0.00667 / 0.33 ( 4) metal coordination : angle 4.32853 / 1.79 ( 6) Misc. bond : bond 0.00020 / 0.01 ( 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 250 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8899 (mtt-85) cc_final: 0.8595 (mtt-85) REVERT: B 59 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8772 (ttpt) REVERT: D 47 GLN cc_start: 0.8196 (tp40) cc_final: 0.7891 (tp40) REVERT: E 73 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8730 (tm-30) REVERT: G 34 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8655 (ttp80) REVERT: G 75 ASP cc_start: 0.7660 (m-30) cc_final: 0.7349 (m-30) REVERT: K 332 PHE cc_start: 0.5572 (m-80) cc_final: 0.4543 (m-80) REVERT: K 348 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7359 (ptpp) outliers start: 17 outliers final: 11 residues processed: 240 average time/residue: 0.1404 time to fit residues: 45.2868 Evaluate side-chains 239 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU 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 H residue 80 LEU Chi-restraints excluded: chain H residue 106 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 85 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.192179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.135118 restraints weight = 29289.318| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.35 r_work: 0.3092 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- 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 = 0.23 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 = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15132 Z= 0.160 Angle : 0.673 8.826 21657 Z= 0.390 Chirality : 0.048 0.291 2438 Planarity : 0.004 0.060 1733 Dihedral : 30.204 156.588 4437 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.20 % Allowed : 14.62 % Favored : 83.18 % 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: 0.09 (0.25), residues: 1027 helix: 1.20 (0.20), residues: 645 sheet: -1.28 (0.79), residues: 26 loop : -2.02 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 286 TYR 0.010 0.001 TYR G 60 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 0.00304 / 0.16 (15126) covalent geometry : angle 0.66905 / 0.39 (21649) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 1.41861 / 0.83 ( 2) hydrogen bonds : bond 0.05779 / 3.90 ( 799) hydrogen bonds : angle 3.61903 / 2.58 ( 2045) metal coordination : bond 0.00604 / 0.30 ( 4) metal coordination : angle 4.11197 / 1.72 ( 6) Misc. bond : bond 0.00040 / 0.02 ( 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 241 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8903 (mtt-85) cc_final: 0.8688 (mtt-85) REVERT: D 47 GLN cc_start: 0.8227 (tp40) cc_final: 0.7879 (tp40) REVERT: E 73 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8802 (tm-30) REVERT: K 332 PHE cc_start: 0.5590 (m-80) cc_final: 0.4562 (m-80) REVERT: K 348 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7369 (ptpp) outliers start: 18 outliers final: 14 residues processed: 228 average time/residue: 0.1311 time to fit residues: 40.6948 Evaluate side-chains 235 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 G residue 109 VAL 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 Chi-restraints excluded: chain K residue 297 ILE 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: 10.0000 chunk 4 optimal weight: 0.4980 chunk 98 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 93 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.188516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.130942 restraints weight = 23866.956| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.04 r_work: 0.3063 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15132 Z= 0.254 Angle : 0.738 8.113 21657 Z= 0.418 Chirality : 0.050 0.312 2438 Planarity : 0.005 0.059 1733 Dihedral : 30.372 157.901 4437 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.55 % Allowed : 15.55 % Favored : 81.90 % 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: -0.33 (0.25), residues: 1027 helix: 0.87 (0.20), residues: 645 sheet: -1.40 (0.79), residues: 26 loop : -2.19 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.013 0.002 TYR E 99 PHE 0.013 0.002 PHE G 27 TRP 0.005 0.001 TRP K 264 HIS 0.006 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.25 (15126) covalent geometry : angle 0.73341 / 0.42 (21649) SS BOND : bond 0.00273 / 0.14 ( 1) SS BOND : angle 1.54381 / 0.90 ( 2) hydrogen bonds : bond 0.06897 / 4.64 ( 799) hydrogen bonds : angle 3.85022 / 2.75 ( 2045) metal coordination : bond 0.00972 / 0.48 ( 4) metal coordination : angle 4.73696 / 1.93 ( 6) Misc. bond : bond 0.00008 / 0.00 ( 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 258 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8497 (mt-10) REVERT: B 79 LYS cc_start: 0.8632 (mmtm) cc_final: 0.7755 (mmtt) REVERT: D 47 GLN cc_start: 0.8201 (tp40) cc_final: 0.7809 (tp40) REVERT: E 73 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8789 (tm-30) REVERT: K 72 MET cc_start: 0.7358 (pmm) cc_final: 0.7058 (pmm) REVERT: K 332 PHE cc_start: 0.5723 (m-80) cc_final: 0.4644 (m-80) REVERT: K 348 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7347 (ptpp) outliers start: 21 outliers final: 20 residues processed: 240 average time/residue: 0.1349 time to fit residues: 43.5105 Evaluate side-chains 252 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 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 E residue 93 GLN 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 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 Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 351 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 30.0000 chunk 47 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.191268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.131172 restraints weight = 20518.369| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.92 r_work: 0.3135 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15132 Z= 0.158 Angle : 0.678 10.488 21657 Z= 0.391 Chirality : 0.048 0.293 2438 Planarity : 0.004 0.050 1733 Dihedral : 30.308 156.598 4437 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.20 % Allowed : 16.01 % Favored : 81.79 % 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: -0.05 (0.25), residues: 1027 helix: 1.08 (0.20), residues: 647 sheet: -1.39 (0.78), residues: 26 loop : -2.07 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.010 0.001 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.005 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (15126) covalent geometry : angle 0.67358 / 0.39 (21649) SS BOND : bond 0.00057 / 0.03 ( 1) SS BOND : angle 1.44416 / 0.85 ( 2) hydrogen bonds : bond 0.05994 / 4.07 ( 799) hydrogen bonds : angle 3.66364 / 2.62 ( 2045) metal coordination : bond 0.00692 / 0.34 ( 4) metal coordination : angle 4.72800 / 1.92 ( 6) Misc. bond : bond 0.00030 / 0.02 ( 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 260 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8566 (mmtm) cc_final: 0.7646 (mmtt) REVERT: D 34 LYS cc_start: 0.7385 (ptpt) cc_final: 0.7009 (pttm) REVERT: D 47 GLN cc_start: 0.8159 (tp40) cc_final: 0.7786 (tp40) REVERT: E 73 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8765 (tm-30) REVERT: K 211 LYS cc_start: 0.6825 (pttt) cc_final: 0.6561 (pttm) REVERT: K 332 PHE cc_start: 0.5578 (m-80) cc_final: 0.4516 (m-80) REVERT: K 348 LYS cc_start: 0.7593 (mtmm) cc_final: 0.7253 (ptpp) outliers start: 18 outliers final: 16 residues processed: 246 average time/residue: 0.1429 time to fit residues: 47.4300 Evaluate side-chains 246 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 56 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 0.0020 chunk 114 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.193885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.132603 restraints weight = 17122.562| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.70 r_work: 0.3188 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15132 Z= 0.146 Angle : 0.663 9.184 21657 Z= 0.383 Chirality : 0.047 0.285 2438 Planarity : 0.004 0.056 1733 Dihedral : 30.229 159.273 4437 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.55 % Allowed : 15.66 % Favored : 81.79 % 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: 0.22 (0.26), residues: 1027 helix: 1.31 (0.20), residues: 646 sheet: -1.27 (0.82), residues: 26 loop : -2.00 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 86 TYR 0.011 0.001 TYR E 54 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP K 264 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (15126) covalent geometry : angle 0.65995 / 0.38 (21649) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 1.33556 / 0.78 ( 2) hydrogen bonds : bond 0.05539 / 3.76 ( 799) hydrogen bonds : angle 3.52927 / 2.52 ( 2045) metal coordination : bond 0.00657 / 0.32 ( 4) metal coordination : angle 3.97995 / 1.67 ( 6) Misc. bond : bond 0.00014 / 0.01 ( 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 250 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: D 34 LYS cc_start: 0.7422 (ptpt) cc_final: 0.7050 (pttm) REVERT: D 47 GLN cc_start: 0.8194 (tp40) cc_final: 0.7944 (tp40) REVERT: E 72 ARG cc_start: 0.9006 (mmt90) cc_final: 0.8774 (mmt90) REVERT: E 73 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8677 (tm-30) REVERT: K 312 PHE cc_start: 0.6482 (m-10) cc_final: 0.6086 (m-10) REVERT: K 332 PHE cc_start: 0.5559 (m-80) cc_final: 0.4494 (m-80) outliers start: 21 outliers final: 18 residues processed: 235 average time/residue: 0.1630 time to fit residues: 51.6434 Evaluate side-chains 245 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 D residue 73 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER 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: 0.9980 chunk 99 optimal weight: 0.5980 chunk 115 optimal weight: 0.0050 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 63 ASN E 93 GLN K 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.194738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.136156 restraints weight = 20666.914| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.93 r_work: 0.3165 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.002 0.036 15132 Z= 0.135 Angle : 0.648 9.162 21657 Z= 0.378 Chirality : 0.046 0.285 2438 Planarity : 0.004 0.044 1733 Dihedral : 30.202 160.900 4437 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.09 % Allowed : 16.36 % Favored : 81.55 % 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: 0.36 (0.26), residues: 1027 helix: 1.43 (0.20), residues: 646 sheet: -1.17 (0.82), 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 0.011 0.001 TYR E 54 PHE 0.012 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 0.00232 / 0.14 (15126) covalent geometry : angle 0.64582 / 0.38 (21649) SS BOND : bond 0.00007 / 0.00 ( 1) SS BOND : angle 1.27058 / 0.74 ( 2) hydrogen bonds : bond 0.05374 / 3.65 ( 799) hydrogen bonds : angle 3.46366 / 2.47 ( 2045) metal coordination : bond 0.00576 / 0.28 ( 4) metal coordination : angle 3.50620 / 1.47 ( 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 240 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8304 (mp10) REVERT: D 34 LYS cc_start: 0.7384 (ptpt) cc_final: 0.6995 (pttm) REVERT: D 47 GLN cc_start: 0.8217 (tp40) cc_final: 0.7981 (tp40) REVERT: E 72 ARG cc_start: 0.8982 (mmt90) cc_final: 0.8734 (mmt90) REVERT: E 73 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8765 (tm-30) REVERT: K 332 PHE cc_start: 0.5450 (m-80) cc_final: 0.4397 (m-80) outliers start: 17 outliers final: 16 residues processed: 227 average time/residue: 0.1394 time to fit residues: 42.9417 Evaluate side-chains 239 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 D residue 87 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER 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: 6.9990 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 80.0000 chunk 106 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN K 181 HIS K 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.192228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132605 restraints weight = 19140.905| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.80 r_work: 0.3139 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- 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 = 0.18 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15132 Z= 0.205 Angle : 0.681 8.845 21657 Z= 0.390 Chirality : 0.047 0.292 2438 Planarity : 0.005 0.043 1733 Dihedral : 30.253 161.835 4437 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.55 % Allowed : 15.89 % Favored : 81.55 % 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: 0.15 (0.25), residues: 1027 helix: 1.25 (0.20), residues: 647 sheet: -1.19 (0.80), residues: 26 loop : -2.05 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 49 TYR 0.012 0.001 TYR E 54 PHE 0.009 0.001 PHE E 67 TRP 0.001 0.001 TRP K 264 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (15126) covalent geometry : angle 0.67804 / 0.39 (21649) SS BOND : bond 0.00241 / 0.13 ( 1) SS BOND : angle 1.30505 / 0.76 ( 2) hydrogen bonds : bond 0.05888 / 3.98 ( 799) hydrogen bonds : angle 3.56434 / 2.54 ( 2045) metal coordination : bond 0.00779 / 0.38 ( 4) metal coordination : angle 3.49741 / 1.43 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3477.97 seconds wall clock time: 60 minutes 6.50 seconds (3606.50 seconds total)