Starting phenix.real_space_refine on Fri Jun 13 20:59:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrd_34053/06_2025/7yrd_34053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrd_34053/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yrd_34053/06_2025/7yrd_34053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrd_34053/06_2025/7yrd_34053.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrd_34053/06_2025/7yrd_34053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrd_34053/06_2025/7yrd_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-5710/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: 9.74, 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: 3.76 Conformation dependent library (CDL) restraints added in 1.4 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: 6.92 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: 5.98 Time building geometry restraints manager: 4.05 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 44.610 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.380 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12104 ( 799) hydrogen bonds : angle 4.97473 ( 2045) metal coordination : bond 0.01063 ( 4) metal coordination : angle 5.08305 ( 6) SS BOND : bond 0.00286 ( 1) SS BOND : angle 0.82369 ( 2) covalent geometry : bond 0.00667 (15126) covalent geometry : angle 0.75517 (21649) 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 : 1.091 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: 0.3694 time to fit residues: 120.2804 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 : 1.112 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.191403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131996 restraints weight = 25038.727| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.19 r_work: 0.3083 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 15132 Z= 0.200 Angle : 0.709 9.886 21657 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 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 799) hydrogen bonds : angle 3.91910 ( 2045) metal coordination : bond 0.00942 ( 4) metal coordination : angle 4.82488 ( 6) SS BOND : bond 0.00012 ( 1) SS BOND : angle 1.67841 ( 2) covalent geometry : bond 0.00444 (15126) covalent geometry : angle 0.70460 (21649) Misc. bond : bond 0.00263 ( 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 249 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8431 (pm20) cc_final: 0.8168 (pm20) REVERT: E 73 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8724 (tm-30) REVERT: G 34 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8759 (ttp80) REVERT: G 75 ASP cc_start: 0.7570 (m-30) cc_final: 0.7360 (m-30) REVERT: H 120 LYS cc_start: 0.7894 (ttmt) cc_final: 0.6777 (tptt) REVERT: K 219 LYS cc_start: 0.7178 (mmmm) cc_final: 0.6650 (mmmm) REVERT: K 332 PHE cc_start: 0.5545 (m-80) cc_final: 0.4445 (m-80) REVERT: K 348 LYS cc_start: 0.7585 (mtmm) cc_final: 0.7368 (ptpp) outliers start: 10 outliers final: 7 residues processed: 241 average time/residue: 0.3971 time to fit residues: 125.7037 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 : 1.617 ------------------------------------------------------------------------------- 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 96 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 10 optimal weight: 0.0270 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 85 optimal weight: 0.0030 chunk 22 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- 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 181 HIS K 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.192922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.133319 restraints weight = 18673.763| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.84 r_work: 0.3161 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15132 Z= 0.169 Angle : 0.660 8.738 21657 Z= 0.383 Chirality : 0.039 0.184 2438 Planarity : 0.006 0.108 1733 Dihedral : 29.890 150.887 4469 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.74 % Allowed : 11.14 % Favored : 87.12 % 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: -0.07 (0.25), residues: 1027 helix: 1.06 (0.20), residues: 645 sheet: -1.23 (0.82), residues: 26 loop : -2.06 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.006 0.001 HIS B 75 PHE 0.013 0.001 PHE K 311 TYR 0.019 0.001 TYR K 254 ARG 0.009 0.001 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.05523 ( 799) hydrogen bonds : angle 3.74253 ( 2045) metal coordination : bond 0.00629 ( 4) metal coordination : angle 4.38143 ( 6) SS BOND : bond 0.00130 ( 1) SS BOND : angle 1.51006 ( 2) covalent geometry : bond 0.00368 (15126) covalent geometry : angle 0.65634 (21649) Misc. bond : bond 0.00164 ( 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 242 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7491 (mmm-85) REVERT: B 59 LYS cc_start: 0.8959 (tttt) cc_final: 0.8703 (tttm) REVERT: D 46 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8024 (mtmt) REVERT: E 73 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8679 (tm-30) REVERT: G 75 ASP cc_start: 0.7569 (m-30) cc_final: 0.7361 (m-30) REVERT: H 120 LYS cc_start: 0.7852 (ttmt) cc_final: 0.6739 (tptt) REVERT: K 72 MET cc_start: 0.7286 (pmm) cc_final: 0.6936 (pmm) REVERT: K 332 PHE cc_start: 0.5508 (m-80) cc_final: 0.4449 (m-80) outliers start: 13 outliers final: 7 residues processed: 234 average time/residue: 0.3903 time to fit residues: 122.2013 Evaluate side-chains 229 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 222 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.188962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.129951 restraints weight = 23752.011| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.10 r_work: 0.3057 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15132 Z= 0.261 Angle : 0.683 8.515 21657 Z= 0.396 Chirality : 0.040 0.204 2438 Planarity : 0.005 0.072 1733 Dihedral : 29.827 153.550 4469 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.74 % Allowed : 12.99 % Favored : 85.27 % 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: -0.27 (0.25), residues: 1027 helix: 0.90 (0.20), residues: 645 sheet: -1.41 (0.78), residues: 26 loop : -2.14 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 264 HIS 0.006 0.001 HIS D 49 PHE 0.010 0.002 PHE E 104 TYR 0.019 0.002 TYR F 88 ARG 0.007 0.001 ARG K 295 Details of bonding type rmsd hydrogen bonds : bond 0.05969 ( 799) hydrogen bonds : angle 3.77553 ( 2045) metal coordination : bond 0.00882 ( 4) metal coordination : angle 4.72098 ( 6) SS BOND : bond 0.00086 ( 1) SS BOND : angle 1.61497 ( 2) covalent geometry : bond 0.00588 (15126) covalent geometry : angle 0.67868 (21649) Misc. bond : bond 0.00044 ( 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 244 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: E 73 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8802 (tm-30) REVERT: G 34 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8765 (ttp80) REVERT: G 75 ASP cc_start: 0.7779 (m-30) cc_final: 0.7465 (m-30) REVERT: K 72 MET cc_start: 0.7293 (pmm) cc_final: 0.6974 (pmm) REVERT: K 332 PHE cc_start: 0.5662 (m-80) cc_final: 0.4575 (m-80) outliers start: 13 outliers final: 10 residues processed: 236 average time/residue: 0.3576 time to fit residues: 113.1109 Evaluate side-chains 235 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 66 LEU 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 129 optimal weight: 0.0470 chunk 116 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 overall best weight: 1.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 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 = 0.190262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.130910 restraints weight = 19256.654| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.85 r_work: 0.3115 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15132 Z= 0.212 Angle : 0.650 8.332 21657 Z= 0.381 Chirality : 0.039 0.200 2438 Planarity : 0.005 0.060 1733 Dihedral : 29.837 152.816 4469 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.09 % Allowed : 13.34 % Favored : 84.57 % 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: -0.15 (0.25), residues: 1027 helix: 0.99 (0.20), residues: 645 sheet: -1.37 (0.78), residues: 26 loop : -2.06 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 264 HIS 0.003 0.001 HIS H 82 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR G 60 ARG 0.008 0.001 ARG B 3 Details of bonding type rmsd hydrogen bonds : bond 0.05541 ( 799) hydrogen bonds : angle 3.68329 ( 2045) metal coordination : bond 0.00777 ( 4) metal coordination : angle 4.72139 ( 6) SS BOND : bond 0.00093 ( 1) SS BOND : angle 1.51398 ( 2) covalent geometry : bond 0.00472 (15126) covalent geometry : angle 0.64489 (21649) Misc. bond : bond 0.00023 ( 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 248 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7464 (mmm-85) REVERT: D 46 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8048 (mtmt) REVERT: E 63 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8506 (mmm160) REVERT: E 73 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8760 (tm-30) REVERT: G 34 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8623 (ttp80) REVERT: K 72 MET cc_start: 0.7254 (pmm) cc_final: 0.6984 (pmm) REVERT: K 332 PHE cc_start: 0.5499 (m-80) cc_final: 0.4438 (m-80) outliers start: 17 outliers final: 15 residues processed: 236 average time/residue: 0.3576 time to fit residues: 112.8488 Evaluate side-chains 239 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 D residue 116 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.184562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.125341 restraints weight = 19260.574| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.96 r_work: 0.3011 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 15132 Z= 0.394 Angle : 0.776 12.758 21657 Z= 0.441 Chirality : 0.045 0.229 2438 Planarity : 0.006 0.078 1733 Dihedral : 30.353 150.672 4469 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.90 % Allowed : 14.50 % Favored : 82.60 % 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: -0.85 (0.24), residues: 1027 helix: 0.46 (0.19), residues: 642 sheet: -1.81 (0.63), residues: 40 loop : -2.37 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 264 HIS 0.008 0.002 HIS G 85 PHE 0.014 0.002 PHE G 27 TYR 0.013 0.002 TYR K 349 ARG 0.006 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.07531 ( 799) hydrogen bonds : angle 4.07226 ( 2045) metal coordination : bond 0.01430 ( 4) metal coordination : angle 7.03938 ( 6) SS BOND : bond 0.00429 ( 1) SS BOND : angle 1.81185 ( 2) covalent geometry : bond 0.00892 (15126) covalent geometry : angle 0.76698 (21649) Misc. bond : bond 0.00039 ( 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 263 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 LYS cc_start: 0.7668 (mttt) cc_final: 0.7437 (mttt) REVERT: D 34 LYS cc_start: 0.7506 (ptpt) cc_final: 0.7051 (pttm) REVERT: D 73 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8192 (mt) REVERT: E 53 ARG cc_start: 0.8259 (ttp-170) cc_final: 0.7981 (ttp-170) REVERT: E 73 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8828 (tm-30) REVERT: G 39 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8343 (tpp80) REVERT: K 72 MET cc_start: 0.7403 (pmm) cc_final: 0.7136 (pmm) REVERT: K 332 PHE cc_start: 0.5759 (m-80) cc_final: 0.5394 (m-80) outliers start: 24 outliers final: 19 residues processed: 245 average time/residue: 0.3619 time to fit residues: 117.7805 Evaluate side-chains 257 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 ARG 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 80 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 351 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS H 109 HIS K 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.193590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134083 restraints weight = 18843.217| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.89 r_work: 0.3178 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1964 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= 0.169 Angle : 0.623 7.747 21657 Z= 0.370 Chirality : 0.038 0.191 2438 Planarity : 0.004 0.042 1733 Dihedral : 29.778 153.106 4469 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.97 % Allowed : 16.24 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.25), residues: 1027 helix: 1.13 (0.20), residues: 647 sheet: -1.47 (0.66), residues: 40 loop : -2.09 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.001 PHE E 67 TYR 0.021 0.001 TYR D 83 ARG 0.007 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 799) hydrogen bonds : angle 3.47938 ( 2045) metal coordination : bond 0.00622 ( 4) metal coordination : angle 3.96032 ( 6) SS BOND : bond 0.00023 ( 1) SS BOND : angle 1.48584 ( 2) covalent geometry : bond 0.00365 (15126) covalent geometry : angle 0.61942 (21649) Misc. bond : bond 0.00046 ( 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 256 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 LYS cc_start: 0.7371 (ptpt) cc_final: 0.6926 (pttm) REVERT: H 51 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7577 (t0) REVERT: K 177 LEU cc_start: 0.6755 (mp) cc_final: 0.6553 (mp) REVERT: K 332 PHE cc_start: 0.5512 (m-80) cc_final: 0.4474 (m-80) outliers start: 16 outliers final: 11 residues processed: 243 average time/residue: 0.3640 time to fit residues: 117.3663 Evaluate side-chains 240 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 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 Chi-restraints excluded: chain K residue 297 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.192835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.134354 restraints weight = 23647.662| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.11 r_work: 0.3122 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15132 Z= 0.186 Angle : 0.621 7.795 21657 Z= 0.366 Chirality : 0.037 0.206 2438 Planarity : 0.004 0.043 1733 Dihedral : 29.746 162.879 4469 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.74 % Allowed : 17.29 % Favored : 80.97 % 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: 0.18 (0.25), residues: 1027 helix: 1.26 (0.20), residues: 648 sheet: -1.19 (0.80), residues: 26 loop : -1.98 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 PHE 0.013 0.001 PHE K 311 TYR 0.028 0.001 TYR D 83 ARG 0.008 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05106 ( 799) hydrogen bonds : angle 3.46157 ( 2045) metal coordination : bond 0.00618 ( 4) metal coordination : angle 3.83000 ( 6) SS BOND : bond 0.00179 ( 1) SS BOND : angle 1.47238 ( 2) covalent geometry : bond 0.00409 (15126) covalent geometry : angle 0.61798 (21649) Misc. bond : bond 0.00038 ( 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 247 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: D 34 LYS cc_start: 0.7381 (ptpt) cc_final: 0.6972 (pttm) REVERT: H 51 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7622 (t0) REVERT: H 105 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8343 (mm-30) REVERT: K 173 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5438 (mmp) REVERT: K 177 LEU cc_start: 0.6714 (mp) cc_final: 0.6503 (mp) REVERT: K 332 PHE cc_start: 0.5589 (m-80) cc_final: 0.4519 (m-80) outliers start: 14 outliers final: 11 residues processed: 233 average time/residue: 0.3529 time to fit residues: 110.0430 Evaluate side-chains 242 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 88 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 173 MET 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 52 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 0.2980 chunk 50 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.196748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.139589 restraints weight = 25306.002| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.12 r_work: 0.3174 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15132 Z= 0.155 Angle : 0.601 7.525 21657 Z= 0.355 Chirality : 0.036 0.189 2438 Planarity : 0.004 0.042 1733 Dihedral : 29.574 169.168 4469 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.62 % Allowed : 17.75 % Favored : 80.63 % 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: 0.45 (0.26), residues: 1027 helix: 1.46 (0.20), residues: 647 sheet: -1.06 (0.83), residues: 26 loop : -1.85 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 PHE 0.012 0.001 PHE K 311 TYR 0.022 0.001 TYR D 83 ARG 0.008 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 799) hydrogen bonds : angle 3.32515 ( 2045) metal coordination : bond 0.00430 ( 4) metal coordination : angle 2.94674 ( 6) SS BOND : bond 0.00042 ( 1) SS BOND : angle 1.32820 ( 2) covalent geometry : bond 0.00333 (15126) covalent geometry : angle 0.59903 (21649) Misc. bond : bond 0.00041 ( 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 235 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8832 (tttp) REVERT: B 78 ARG cc_start: 0.8902 (ptt180) cc_final: 0.8668 (ptt90) REVERT: D 34 LYS cc_start: 0.7398 (ptpt) cc_final: 0.6977 (pttm) REVERT: E 73 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8774 (tm-30) REVERT: K 173 MET cc_start: 0.5845 (OUTLIER) cc_final: 0.5432 (mmp) REVERT: K 177 LEU cc_start: 0.6799 (mp) cc_final: 0.6598 (mp) REVERT: K 332 PHE cc_start: 0.5494 (m-80) cc_final: 0.4420 (m-80) outliers start: 13 outliers final: 9 residues processed: 225 average time/residue: 0.3561 time to fit residues: 107.9098 Evaluate side-chains 229 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 88 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain K residue 173 MET 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 45 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.193721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.135349 restraints weight = 23676.627| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.07 r_work: 0.3131 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15132 Z= 0.195 Angle : 0.626 8.055 21657 Z= 0.365 Chirality : 0.037 0.210 2438 Planarity : 0.004 0.044 1733 Dihedral : 29.640 170.722 4469 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.16 % Allowed : 18.10 % Favored : 80.74 % 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: 0.32 (0.25), residues: 1027 helix: 1.35 (0.20), residues: 647 sheet: -1.00 (0.80), residues: 26 loop : -1.88 (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 G 85 PHE 0.012 0.001 PHE K 311 TYR 0.023 0.001 TYR D 83 ARG 0.007 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 799) hydrogen bonds : angle 3.45590 ( 2045) metal coordination : bond 0.00574 ( 4) metal coordination : angle 3.44281 ( 6) SS BOND : bond 0.00123 ( 1) SS BOND : angle 1.35286 ( 2) covalent geometry : bond 0.00432 (15126) covalent geometry : angle 0.62335 (21649) 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 230 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 221 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: D 34 LYS cc_start: 0.7462 (ptpt) cc_final: 0.7067 (pttm) REVERT: E 73 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8787 (tm-30) REVERT: K 173 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5416 (mmp) REVERT: K 177 LEU cc_start: 0.6837 (mp) cc_final: 0.6594 (mp) REVERT: K 332 PHE cc_start: 0.5583 (m-80) cc_final: 0.4485 (m-80) outliers start: 9 outliers final: 8 residues processed: 224 average time/residue: 0.3301 time to fit residues: 100.8745 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 : 1.197 ------------------------------------------------------------------------------- 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 88 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain K residue 173 MET 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 127 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.197221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.138495 restraints weight = 21137.564| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.95 r_work: 0.3200 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15132 Z= 0.157 Angle : 0.602 7.727 21657 Z= 0.353 Chirality : 0.036 0.189 2438 Planarity : 0.004 0.044 1733 Dihedral : 29.476 172.685 4469 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.39 % Allowed : 17.75 % Favored : 80.86 % 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: 0.54 (0.26), residues: 1027 helix: 1.53 (0.20), residues: 647 sheet: -0.87 (0.83), residues: 26 loop : -1.84 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.021 0.001 TYR D 83 ARG 0.008 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 799) hydrogen bonds : angle 3.33414 ( 2045) metal coordination : bond 0.00442 ( 4) metal coordination : angle 2.92149 ( 6) SS BOND : bond 0.00023 ( 1) SS BOND : angle 1.30303 ( 2) covalent geometry : bond 0.00341 (15126) covalent geometry : angle 0.59960 (21649) Misc. bond : bond 0.00056 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8430.75 seconds wall clock time: 146 minutes 38.84 seconds (8798.84 seconds total)