Starting phenix.real_space_refine on Sat Aug 23 23:30:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrd_34053/08_2025/7yrd_34053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrd_34053/08_2025/7yrd_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_2025/7yrd_34053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2025/7yrd_34053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2025/7yrd_34053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrd_34053/08_2025/7yrd_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-2.0-5787/lib/python3.9/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: 3.23, per 1000 atoms: 0.23 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: 0.86 Conformation dependent library (CDL) restraints added in 371.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.63 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: 1.99 Time building geometry restraints manager: 1.14 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- 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 0.286 15132 Z= 0.416 Angle : 0.760 11.650 21657 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00667 (15126) covalent geometry : angle 0.75517 (21649) SS BOND : bond 0.00286 ( 1) SS BOND : angle 0.82369 ( 2) hydrogen bonds : bond 0.12104 ( 799) hydrogen bonds : angle 4.97473 ( 2045) metal coordination : bond 0.01063 ( 4) metal coordination : angle 5.08305 ( 6) Misc. bond : bond 0.28575 ( 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 : 0.304 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: 0.1417 time to fit residues: 46.5976 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 : 0.271 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 84 ASN D 109 HIS K 259 ASN K 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.191950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132460 restraints weight = 23776.585| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.12 r_work: 0.3093 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15132 Z= 0.188 Angle : 0.678 9.980 21657 Z= 0.393 Chirality : 0.039 0.190 2438 Planarity : 0.005 0.081 1733 Dihedral : 29.901 150.423 4469 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.70 % Allowed : 10.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.25), residues: 1027 helix: 0.94 (0.20), residues: 645 sheet: -1.27 (0.69), residues: 40 loop : -2.14 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 326 TYR 0.026 0.001 TYR K 254 PHE 0.016 0.001 PHE K 311 TRP 0.006 0.001 TRP K 264 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (15126) covalent geometry : angle 0.67222 (21649) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.76942 ( 2) hydrogen bonds : bond 0.05857 ( 799) hydrogen bonds : angle 3.79497 ( 2045) metal coordination : bond 0.00804 ( 4) metal coordination : angle 5.35395 ( 6) Misc. bond : bond 0.00199 ( 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 241 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8523 (pm20) cc_final: 0.8263 (pm20) REVERT: A 134 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: B 59 LYS cc_start: 0.8921 (tttt) cc_final: 0.8690 (tttt) REVERT: E 73 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8717 (tm-30) REVERT: G 75 ASP cc_start: 0.7643 (m-30) cc_final: 0.7407 (m-30) REVERT: K 219 LYS cc_start: 0.7226 (mmmm) cc_final: 0.6713 (mmmm) REVERT: K 332 PHE cc_start: 0.5538 (m-80) cc_final: 0.4446 (m-80) outliers start: 4 outliers final: 3 residues processed: 238 average time/residue: 0.1446 time to fit residues: 45.8674 Evaluate side-chains 223 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR 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: 7.9990 chunk 97 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.190410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.131195 restraints weight = 17177.270| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.86 r_work: 0.3137 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15132 Z= 0.220 Angle : 0.656 9.206 21657 Z= 0.383 Chirality : 0.039 0.197 2438 Planarity : 0.005 0.049 1733 Dihedral : 29.777 154.020 4469 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.97 % Allowed : 11.95 % Favored : 86.08 % 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 aren not related in a simple way. whole: -0.12 (0.25), residues: 1027 helix: 1.01 (0.20), residues: 645 sheet: -1.33 (0.77), residues: 26 loop : -2.07 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 326 TYR 0.011 0.001 TYR G 60 PHE 0.010 0.001 PHE K 311 TRP 0.007 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00489 (15126) covalent geometry : angle 0.65077 (21649) SS BOND : bond 0.00099 ( 1) SS BOND : angle 1.82335 ( 2) hydrogen bonds : bond 0.05543 ( 799) hydrogen bonds : angle 3.68473 ( 2045) metal coordination : bond 0.00865 ( 4) metal coordination : angle 4.75372 ( 6) Misc. bond : bond 0.00152 ( 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 246 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7480 (mmm-85) REVERT: E 73 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8718 (tm-30) REVERT: G 34 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8671 (ttp80) REVERT: G 75 ASP cc_start: 0.7639 (m-30) cc_final: 0.7351 (m-30) REVERT: K 332 PHE cc_start: 0.5588 (m-80) cc_final: 0.4516 (m-80) outliers start: 15 outliers final: 12 residues processed: 235 average time/residue: 0.1452 time to fit residues: 45.6330 Evaluate side-chains 235 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 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 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 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: 0.8980 chunk 111 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.190741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132815 restraints weight = 23912.212| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.14 r_work: 0.3074 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15132 Z= 0.209 Angle : 0.642 8.398 21657 Z= 0.377 Chirality : 0.039 0.204 2438 Planarity : 0.005 0.061 1733 Dihedral : 29.793 155.458 4469 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.44 % Allowed : 13.34 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.25), residues: 1027 helix: 1.07 (0.20), residues: 645 sheet: -1.21 (0.77), residues: 26 loop : -2.04 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 326 TYR 0.010 0.001 TYR G 60 PHE 0.010 0.001 PHE K 311 TRP 0.005 0.001 TRP K 264 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00465 (15126) covalent geometry : angle 0.63669 (21649) SS BOND : bond 0.00078 ( 1) SS BOND : angle 1.56686 ( 2) hydrogen bonds : bond 0.05404 ( 799) hydrogen bonds : angle 3.60081 ( 2045) metal coordination : bond 0.00790 ( 4) metal coordination : angle 4.73905 ( 6) Misc. bond : bond 0.00040 ( 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 246 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8909 (mtt-85) cc_final: 0.8632 (mtt-85) REVERT: E 63 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8557 (mmm160) REVERT: E 73 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8800 (tm-30) REVERT: G 34 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8707 (ttp80) REVERT: K 219 LYS cc_start: 0.7296 (mmmm) cc_final: 0.6735 (mmmm) REVERT: K 332 PHE cc_start: 0.5546 (m-80) cc_final: 0.4495 (m-80) outliers start: 20 outliers final: 14 residues processed: 233 average time/residue: 0.1739 time to fit residues: 53.2281 Evaluate side-chains 237 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 K 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.195112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136808 restraints weight = 20816.228| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.95 r_work: 0.3173 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15132 Z= 0.166 Angle : 0.602 7.636 21657 Z= 0.359 Chirality : 0.037 0.192 2438 Planarity : 0.004 0.042 1733 Dihedral : 29.582 166.417 4469 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.86 % Allowed : 14.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1027 helix: 1.40 (0.20), residues: 646 sheet: -1.09 (0.79), residues: 26 loop : -1.87 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 286 TYR 0.010 0.001 TYR G 60 PHE 0.009 0.001 PHE E 67 TRP 0.006 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00361 (15126) covalent geometry : angle 0.59934 (21649) SS BOND : bond 0.00034 ( 1) SS BOND : angle 1.53960 ( 2) hydrogen bonds : bond 0.04689 ( 799) hydrogen bonds : angle 3.36734 ( 2045) metal coordination : bond 0.00523 ( 4) metal coordination : angle 3.31041 ( 6) Misc. bond : bond 0.00012 ( 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 246 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8804 (mtt-85) cc_final: 0.8531 (mtt-85) REVERT: B 82 THR cc_start: 0.9214 (t) cc_final: 0.8937 (p) REVERT: D 34 LYS cc_start: 0.7344 (ptpt) cc_final: 0.6969 (pttm) REVERT: K 219 LYS cc_start: 0.7249 (mmmm) cc_final: 0.6657 (mmmm) REVERT: K 332 PHE cc_start: 0.5421 (m-80) cc_final: 0.4360 (m-80) outliers start: 15 outliers final: 9 residues processed: 236 average time/residue: 0.1670 time to fit residues: 51.7461 Evaluate side-chains 231 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 228 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 68 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 = 0.4066 r_free = 0.4066 target = 0.195487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.139427 restraints weight = 29162.778| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.43 r_work: 0.3136 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- 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 = 0.25 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15132 Z= 0.168 Angle : 0.598 7.189 21657 Z= 0.355 Chirality : 0.036 0.198 2438 Planarity : 0.004 0.060 1733 Dihedral : 29.560 169.943 4469 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.97 % Allowed : 14.62 % Favored : 83.41 % 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 aren not related in a simple way. whole: 0.46 (0.26), residues: 1027 helix: 1.45 (0.20), residues: 648 sheet: -1.11 (0.80), residues: 26 loop : -1.82 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 326 TYR 0.009 0.001 TYR G 60 PHE 0.014 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 covalent geometry : bond 0.00367 (15126) covalent geometry : angle 0.59568 (21649) SS BOND : bond 0.00037 ( 1) SS BOND : angle 1.47360 ( 2) hydrogen bonds : bond 0.04730 ( 799) hydrogen bonds : angle 3.35495 ( 2045) metal coordination : bond 0.00547 ( 4) metal coordination : angle 3.36490 ( 6) Misc. bond : bond 0.00028 ( 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 238 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 22 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8599 (ttm170) REVERT: K 332 PHE cc_start: 0.5506 (m-80) cc_final: 0.4440 (m-80) outliers start: 16 outliers final: 10 residues processed: 230 average time/residue: 0.1558 time to fit residues: 47.7938 Evaluate side-chains 228 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 228 VAL Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3981 r_free = 0.3981 target = 0.187329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.128258 restraints weight = 23686.913| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.22 r_work: 0.3029 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 15132 Z= 0.331 Angle : 0.719 10.287 21657 Z= 0.411 Chirality : 0.042 0.230 2438 Planarity : 0.005 0.070 1733 Dihedral : 30.047 165.372 4469 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.55 % Allowed : 15.31 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.25), residues: 1027 helix: 0.87 (0.20), residues: 641 sheet: -1.37 (0.75), residues: 26 loop : -2.06 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 326 TYR 0.012 0.002 TYR F 51 PHE 0.011 0.002 PHE E 104 TRP 0.007 0.001 TRP K 264 HIS 0.007 0.002 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00751 (15126) covalent geometry : angle 0.71232 (21649) SS BOND : bond 0.00276 ( 1) SS BOND : angle 1.80500 ( 2) hydrogen bonds : bond 0.06672 ( 799) hydrogen bonds : angle 3.82048 ( 2045) metal coordination : bond 0.01160 ( 4) metal coordination : angle 5.94473 ( 6) Misc. bond : bond 0.00042 ( 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 265 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: D 34 LYS cc_start: 0.7468 (ptpt) cc_final: 0.7071 (pttm) REVERT: D 73 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8180 (mt) REVERT: E 73 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8808 (tm-30) REVERT: E 82 LEU cc_start: 0.9599 (tp) cc_final: 0.9384 (mp) REVERT: K 72 MET cc_start: 0.7344 (pmm) cc_final: 0.7053 (pmm) REVERT: K 332 PHE cc_start: 0.5722 (m-80) cc_final: 0.5343 (m-80) outliers start: 21 outliers final: 18 residues processed: 253 average time/residue: 0.1674 time to fit residues: 56.6790 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 : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain 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 51 ASP 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 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL 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: 0.9980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.194579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.135882 restraints weight = 20348.817| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.96 r_work: 0.3160 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15132 Z= 0.166 Angle : 0.613 7.232 21657 Z= 0.361 Chirality : 0.037 0.194 2438 Planarity : 0.004 0.044 1733 Dihedral : 29.671 170.098 4469 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.97 % Allowed : 16.71 % Favored : 81.32 % 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 aren not related in a simple way. whole: 0.26 (0.25), residues: 1027 helix: 1.30 (0.20), residues: 645 sheet: -1.15 (0.79), residues: 26 loop : -1.88 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.031 0.001 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00359 (15126) covalent geometry : angle 0.60896 (21649) SS BOND : bond 0.00002 ( 1) SS BOND : angle 1.53183 ( 2) hydrogen bonds : bond 0.04859 ( 799) hydrogen bonds : angle 3.41139 ( 2045) metal coordination : bond 0.00634 ( 4) metal coordination : angle 4.01419 ( 6) Misc. bond : bond 0.00041 ( 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 238 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8725 (mtt-85) cc_final: 0.8521 (mtt-85) REVERT: D 34 LYS cc_start: 0.7373 (ptpt) cc_final: 0.6944 (pttm) REVERT: K 219 LYS cc_start: 0.7286 (mmmm) cc_final: 0.6699 (mmmm) REVERT: K 332 PHE cc_start: 0.5516 (m-80) cc_final: 0.4442 (m-80) outliers start: 16 outliers final: 9 residues processed: 230 average time/residue: 0.1600 time to fit residues: 49.2966 Evaluate side-chains 227 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 109 VAL Chi-restraints excluded: chain H residue 112 SER 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: 0.9980 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.197760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.136625 restraints weight = 17039.054| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.70 r_work: 0.3236 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2515 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 : 0.595 7.512 21657 Z= 0.349 Chirality : 0.036 0.195 2438 Planarity : 0.004 0.043 1733 Dihedral : 29.469 174.471 4469 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.04 % Allowed : 17.75 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1027 helix: 1.51 (0.20), residues: 647 sheet: -1.02 (0.82), residues: 26 loop : -1.78 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 49 TYR 0.031 0.001 TYR D 83 PHE 0.011 0.001 PHE K 311 TRP 0.008 0.001 TRP K 264 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (15126) covalent geometry : angle 0.59353 (21649) SS BOND : bond 0.00043 ( 1) SS BOND : angle 1.44952 ( 2) hydrogen bonds : bond 0.04492 ( 799) hydrogen bonds : angle 3.30831 ( 2045) metal coordination : bond 0.00443 ( 4) metal coordination : angle 2.63327 ( 6) Misc. bond : bond 0.00054 ( 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 227 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8738 (mtt-85) cc_final: 0.8485 (mtt-85) REVERT: D 34 LYS cc_start: 0.7413 (ptpt) cc_final: 0.7043 (pttm) REVERT: E 55 GLN cc_start: 0.9271 (mt0) cc_final: 0.8937 (mt0) REVERT: E 73 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8715 (tm-30) REVERT: G 75 ASP cc_start: 0.7744 (m-30) cc_final: 0.7523 (m-30) REVERT: H 46 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8321 (mmmt) REVERT: K 72 MET cc_start: 0.7176 (pmm) cc_final: 0.6901 (pmm) REVERT: K 219 LYS cc_start: 0.7347 (mmmm) cc_final: 0.6807 (mmmm) REVERT: K 311 PHE cc_start: 0.6791 (t80) cc_final: 0.6545 (t80) outliers start: 8 outliers final: 5 residues processed: 224 average time/residue: 0.1456 time to fit residues: 44.0180 Evaluate side-chains 221 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 216 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 73 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.198092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139551 restraints weight = 20611.910| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.93 r_work: 0.3205 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15132 Z= 0.158 Angle : 0.598 8.648 21657 Z= 0.349 Chirality : 0.036 0.196 2438 Planarity : 0.004 0.044 1733 Dihedral : 29.447 174.475 4469 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.04 % Allowed : 17.75 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.26), residues: 1027 helix: 1.57 (0.20), residues: 647 sheet: -0.85 (0.83), residues: 26 loop : -1.73 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 49 TYR 0.028 0.001 TYR D 83 PHE 0.010 0.001 PHE K 311 TRP 0.007 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00343 (15126) covalent geometry : angle 0.59632 (21649) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.63276 ( 2) hydrogen bonds : bond 0.04440 ( 799) hydrogen bonds : angle 3.30890 ( 2045) metal coordination : bond 0.00447 ( 4) metal coordination : angle 2.77157 ( 6) Misc. bond : bond 0.00044 ( 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 227 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8416 (mtt-85) REVERT: D 34 LYS cc_start: 0.7359 (ptpt) cc_final: 0.6950 (pttm) REVERT: E 55 GLN cc_start: 0.9260 (mt0) cc_final: 0.8974 (mt0) REVERT: E 134 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7044 (ttp80) REVERT: G 75 ASP cc_start: 0.7625 (m-30) cc_final: 0.7406 (m-30) REVERT: K 219 LYS cc_start: 0.7294 (mmmm) cc_final: 0.6683 (mmmm) REVERT: K 311 PHE cc_start: 0.6886 (t80) cc_final: 0.6569 (t80) outliers start: 8 outliers final: 7 residues processed: 225 average time/residue: 0.1597 time to fit residues: 48.9045 Evaluate side-chains 224 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain G residue 109 VAL 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 69 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 100.0000 chunk 106 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.194277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134576 restraints weight = 19055.088| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.83 r_work: 0.3157 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15132 Z= 0.206 Angle : 0.636 9.605 21657 Z= 0.365 Chirality : 0.038 0.250 2438 Planarity : 0.005 0.045 1733 Dihedral : 29.609 173.626 4469 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.04 % Allowed : 17.75 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1027 helix: 1.39 (0.20), residues: 645 sheet: -0.97 (0.80), residues: 26 loop : -1.85 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.031 0.002 TYR D 83 PHE 0.009 0.001 PHE K 311 TRP 0.004 0.001 TRP K 264 HIS 0.003 0.001 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00460 (15126) covalent geometry : angle 0.63275 (21649) SS BOND : bond 0.00060 ( 1) SS BOND : angle 1.61962 ( 2) hydrogen bonds : bond 0.05111 ( 799) hydrogen bonds : angle 3.49662 ( 2045) metal coordination : bond 0.00605 ( 4) metal coordination : angle 3.68084 ( 6) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3667.18 seconds wall clock time: 63 minutes 17.08 seconds (3797.08 seconds total)