Starting phenix.real_space_refine on Tue Dec 31 10:17:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrd_34053/12_2024/7yrd_34053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrd_34053/12_2024/7yrd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yrd_34053/12_2024/7yrd_34053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrd_34053/12_2024/7yrd_34053.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrd_34053/12_2024/7yrd_34053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrd_34053/12_2024/7yrd_34053.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 4, 'ARG:plan': 2, '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: {'GLU:plan': 4, 'ARG:plan': 2, '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: 9.67, per 1000 atoms: 0.68 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: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 6.81 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: 5.95 Time building geometry restraints manager: 3.94 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: 21289 2.33 - 4.66: 307 4.66 - 6.99: 35 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: 6761 31.24 - 62.49: 1626 62.49 - 93.73: 59 93.73 - 124.98: 1 124.98 - 156.22: 4 Dihedral angle restraints: 8451 sinusoidal: 5419 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 8448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2367 0.103 - 0.207: 66 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.620 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.007 0.148 15126 Z= 0.443 Angle : 0.755 11.650 21649 Z= 0.439 Chirality : 0.044 0.517 2438 Planarity : 0.005 0.073 1733 Dihedral : 26.757 156.219 6496 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (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 TRP 0.007 0.001 TRP K 264 HIS 0.010 0.001 HIS B 75 PHE 0.013 0.002 PHE K 154 TYR 0.012 0.002 TYR G 60 ARG 0.011 0.001 ARG K 357 *********************** 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 : 1.278 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: 0.7561 (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: 0.3895 time to fit residues: 126.9999 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 : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN D 109 HIS K 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15126 Z= 0.256 Angle : 0.705 9.886 21649 Z= 0.409 Chirality : 0.041 0.272 2438 Planarity : 0.006 0.070 1733 Dihedral : 30.057 152.911 4469 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.39 % Allowed : 9.51 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1027 helix: 0.80 (0.20), residues: 644 sheet: -1.11 (0.81), residues: 26 loop : -2.05 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 264 HIS 0.008 0.001 HIS B 75 PHE 0.014 0.001 PHE K 281 TYR 0.011 0.001 TYR F 88 ARG 0.007 0.001 ARG K 357 *********************** 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 249 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8302 (pm20) cc_final: 0.8082 (pm20) REVERT: D 47 GLN cc_start: 0.7605 (tp40) cc_final: 0.7404 (tp40) REVERT: E 73 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8232 (tm-30) REVERT: G 75 ASP cc_start: 0.7480 (m-30) cc_final: 0.7263 (m-30) REVERT: H 120 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7008 (tptt) REVERT: K 219 LYS cc_start: 0.7582 (mmmm) cc_final: 0.7039 (mmmm) REVERT: K 332 PHE cc_start: 0.5979 (m-80) cc_final: 0.5151 (m-80) outliers start: 10 outliers final: 7 residues processed: 241 average time/residue: 0.4149 time to fit residues: 131.8192 Evaluate side-chains 235 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 228 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 43 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 65 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 118 optimal weight: 0.0970 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 0.0070 chunk 117 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 68 GLN K 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15126 Z= 0.230 Angle : 0.651 9.294 21649 Z= 0.382 Chirality : 0.039 0.184 2438 Planarity : 0.005 0.070 1733 Dihedral : 29.859 150.919 4469 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.86 % Allowed : 11.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1027 helix: 1.02 (0.20), residues: 645 sheet: -1.28 (0.81), residues: 26 loop : -2.07 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 264 HIS 0.006 0.001 HIS B 75 PHE 0.014 0.001 PHE K 311 TYR 0.015 0.001 TYR K 254 ARG 0.020 0.001 ARG K 295 *********************** 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 245 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.7268 (mmm-85) REVERT: D 47 GLN cc_start: 0.7611 (tp40) cc_final: 0.7371 (tp40) REVERT: E 73 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8227 (tm-30) REVERT: G 75 ASP cc_start: 0.7518 (m-30) cc_final: 0.7314 (m-30) REVERT: H 120 LYS cc_start: 0.7900 (ttmt) cc_final: 0.6981 (tptt) REVERT: K 332 PHE cc_start: 0.5989 (m-80) cc_final: 0.5163 (m-80) outliers start: 14 outliers final: 8 residues processed: 237 average time/residue: 0.3765 time to fit residues: 119.1577 Evaluate side-chains 232 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 G residue 109 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.0570 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15126 Z= 0.223 Angle : 0.631 8.369 21649 Z= 0.375 Chirality : 0.038 0.195 2438 Planarity : 0.005 0.072 1733 Dihedral : 29.662 153.717 4469 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.74 % Allowed : 13.34 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1027 helix: 1.18 (0.20), residues: 644 sheet: -1.37 (0.81), residues: 26 loop : -2.02 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE K 311 TYR 0.022 0.001 TYR F 88 ARG 0.010 0.001 ARG B 3 *********************** 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 232 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7253 (mmm-85) REVERT: D 47 GLN cc_start: 0.7668 (tp40) cc_final: 0.7446 (tp40) REVERT: E 63 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.8273 (mmm160) REVERT: E 73 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8242 (tm-30) REVERT: G 75 ASP cc_start: 0.7515 (m-30) cc_final: 0.7261 (m-30) REVERT: H 120 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7016 (tptt) REVERT: K 332 PHE cc_start: 0.5916 (m-80) cc_final: 0.5098 (m-80) outliers start: 13 outliers final: 11 residues processed: 222 average time/residue: 0.3725 time to fit residues: 110.7024 Evaluate side-chains 224 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 112 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15126 Z= 0.211 Angle : 0.616 7.818 21649 Z= 0.367 Chirality : 0.037 0.196 2438 Planarity : 0.004 0.074 1733 Dihedral : 29.645 157.961 4469 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.20 % Allowed : 13.69 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1027 helix: 1.33 (0.20), residues: 644 sheet: -1.27 (0.81), residues: 26 loop : -1.97 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE K 311 TYR 0.020 0.001 TYR F 88 ARG 0.006 0.000 ARG E 49 *********************** 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 235 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7259 (mmm-85) REVERT: E 73 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8224 (tm-30) REVERT: G 75 ASP cc_start: 0.7545 (m-30) cc_final: 0.7254 (m-30) REVERT: H 120 LYS cc_start: 0.7930 (ttmt) cc_final: 0.6994 (tptt) REVERT: K 332 PHE cc_start: 0.5869 (m-80) cc_final: 0.5044 (m-80) outliers start: 18 outliers final: 11 residues processed: 223 average time/residue: 0.3454 time to fit residues: 105.3323 Evaluate side-chains 221 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 E residue 35 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 106 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN K 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15126 Z= 0.217 Angle : 0.616 8.301 21649 Z= 0.366 Chirality : 0.037 0.194 2438 Planarity : 0.004 0.064 1733 Dihedral : 29.629 160.860 4469 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.86 % Allowed : 14.15 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1027 helix: 1.37 (0.20), residues: 644 sheet: -1.33 (0.70), residues: 40 loop : -2.02 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE K 311 TYR 0.010 0.001 TYR G 60 ARG 0.007 0.001 ARG K 326 *********************** 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 229 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8138 (mtmt) REVERT: E 73 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8269 (tm-30) REVERT: G 75 ASP cc_start: 0.7561 (m-30) cc_final: 0.7244 (m-30) REVERT: H 120 LYS cc_start: 0.7902 (ttmt) cc_final: 0.6974 (tptt) REVERT: K 332 PHE cc_start: 0.5866 (m-80) cc_final: 0.5044 (m-80) outliers start: 15 outliers final: 13 residues processed: 220 average time/residue: 0.3497 time to fit residues: 104.5301 Evaluate side-chains 224 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 116 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER 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 121 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 57 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15126 Z= 0.172 Angle : 0.583 6.817 21649 Z= 0.349 Chirality : 0.036 0.181 2438 Planarity : 0.004 0.042 1733 Dihedral : 29.446 171.545 4469 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.74 % Allowed : 14.39 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1027 helix: 1.67 (0.20), residues: 648 sheet: -1.28 (0.72), residues: 40 loop : -1.87 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 264 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.008 0.001 TYR E 54 ARG 0.009 0.001 ARG E 49 *********************** 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 238 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 224 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7774 (mtmt) REVERT: G 75 ASP cc_start: 0.7508 (m-30) cc_final: 0.7246 (m-30) REVERT: H 120 LYS cc_start: 0.7838 (ttmt) cc_final: 0.6909 (tptt) REVERT: K 332 PHE cc_start: 0.5842 (m-80) cc_final: 0.5042 (m-80) outliers start: 14 outliers final: 9 residues processed: 226 average time/residue: 0.3824 time to fit residues: 116.6554 Evaluate side-chains 223 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU 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 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.0870 chunk 85 optimal weight: 0.0370 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 0.0970 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15126 Z= 0.167 Angle : 0.570 7.358 21649 Z= 0.339 Chirality : 0.035 0.186 2438 Planarity : 0.004 0.042 1733 Dihedral : 29.257 174.800 4469 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.28 % Allowed : 15.20 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1027 helix: 1.78 (0.20), residues: 653 sheet: -1.10 (0.86), residues: 26 loop : -1.69 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR F 88 ARG 0.007 0.000 ARG E 49 *********************** 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 221 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8181 (tm-30) REVERT: G 75 ASP cc_start: 0.7523 (m-30) cc_final: 0.7298 (m-30) REVERT: H 120 LYS cc_start: 0.7812 (ttmt) cc_final: 0.6881 (tptt) REVERT: K 177 LEU cc_start: 0.7581 (mp) cc_final: 0.7320 (mp) outliers start: 10 outliers final: 9 residues processed: 215 average time/residue: 0.3748 time to fit residues: 109.4073 Evaluate side-chains 214 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 271 ILE 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 109 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 105 optimal weight: 0.0870 chunk 110 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15126 Z= 0.186 Angle : 0.578 7.284 21649 Z= 0.341 Chirality : 0.035 0.189 2438 Planarity : 0.004 0.046 1733 Dihedral : 29.269 175.000 4469 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.28 % Allowed : 15.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1027 helix: 1.76 (0.20), residues: 652 sheet: -1.04 (0.84), residues: 26 loop : -1.63 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR E 54 ARG 0.011 0.000 ARG A 131 *********************** 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 217 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: G 75 ASP cc_start: 0.7578 (m-30) cc_final: 0.7358 (m-30) REVERT: H 120 LYS cc_start: 0.7782 (ttmt) cc_final: 0.6835 (tptt) REVERT: K 177 LEU cc_start: 0.7557 (mp) cc_final: 0.7301 (mp) outliers start: 10 outliers final: 8 residues processed: 211 average time/residue: 0.3495 time to fit residues: 99.9037 Evaluate side-chains 214 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 129 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15126 Z= 0.177 Angle : 0.574 7.691 21649 Z= 0.338 Chirality : 0.035 0.188 2438 Planarity : 0.004 0.042 1733 Dihedral : 29.222 175.208 4469 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.16 % Allowed : 16.13 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1027 helix: 1.81 (0.20), residues: 650 sheet: -1.01 (0.86), residues: 26 loop : -1.63 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.014 0.001 TYR E 54 ARG 0.008 0.000 ARG A 131 ********************** 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 212 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8221 (tm-30) REVERT: H 120 LYS cc_start: 0.7765 (ttmt) cc_final: 0.6824 (tptt) REVERT: K 177 LEU cc_start: 0.7587 (mp) cc_final: 0.7322 (mp) outliers start: 9 outliers final: 8 residues processed: 206 average time/residue: 0.3712 time to fit residues: 106.0959 Evaluate side-chains 210 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.199787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.143828 restraints weight = 25308.143| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.22 r_work: 0.3197 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15126 Z= 0.213 Angle : 0.594 9.936 21649 Z= 0.347 Chirality : 0.035 0.200 2438 Planarity : 0.004 0.043 1733 Dihedral : 29.262 174.998 4469 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.28 % Allowed : 16.24 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1027 helix: 1.74 (0.20), residues: 647 sheet: -0.95 (0.83), residues: 26 loop : -1.67 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE K 281 TYR 0.019 0.001 TYR F 88 ARG 0.008 0.001 ARG E 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.15 seconds wall clock time: 56 minutes 57.75 seconds (3417.75 seconds total)