Starting phenix.real_space_refine on Thu Jul 2 17:05:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9u_31827/07_2026/7v9u_31827.cif" } resolution = 3.12 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= 0.003 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 209 5.49 5 S 18 5.16 5 C 5183 2.51 5 N 1687 2.21 5 O 2257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9354 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2478 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "B" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2478 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "D" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1205 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 22, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 45} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 10, 'rna3p_pur': 21, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 43} Chain breaks: 1 Chain: "H" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9354 At special positions: 0 Unit cell: (123.25, 153, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 209 15.00 O 2257 8.00 N 1687 7.00 C 5183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 145.6 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 58.6% alpha, 9.4% beta 65 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.725A pdb=" N ASN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.674A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.645A pdb=" N PHE A 46 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.521A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.905A pdb=" N LEU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.728A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.662A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.644A pdb=" N ASP A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 224 removed outlier: 3.588A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.998A pdb=" N GLY A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 3.813A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.732A pdb=" N ILE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 310 removed outlier: 3.812A pdb=" N HIS A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.706A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.544A pdb=" N PHE B 46 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.576A pdb=" N ALA B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.508A pdb=" N ALA B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.735A pdb=" N PHE B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.653A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.633A pdb=" N ASP B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.644A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 257 through 272 removed outlier: 4.795A pdb=" N ILE B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.146A pdb=" N HIS B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 281' Processing helix chain 'B' and resid 284 through 292 removed outlier: 4.025A pdb=" N ILE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.641A pdb=" N HIS B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 53 removed outlier: 3.784A pdb=" N ARG A 63 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 121 removed outlier: 4.733A pdb=" N VAL A 226 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.951A pdb=" N ARG B 61 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195 removed outlier: 3.575A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 121 removed outlier: 4.761A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 226 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1851 1.33 - 1.45: 3295 1.45 - 1.57: 4394 1.57 - 1.69: 408 1.69 - 1.81: 26 Bond restraints: 9974 Sorted by residual: bond pdb=" C3' DG D 73 " pdb=" C2' DG D 73 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.40e+00 bond pdb=" C3' DA C 7 " pdb=" C2' DA C 7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.71e+00 bond pdb=" C3' DG C 73 " pdb=" C2' DG C 73 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 bond pdb=" C4' DC C 83 " pdb=" C3' DC C 83 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.00e-02 1.00e+04 8.29e+00 bond pdb=" C3' DA D 7 " pdb=" C2' DA D 7 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 ... (remaining 9969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 13757 1.51 - 3.01: 562 3.01 - 4.52: 75 4.52 - 6.02: 18 6.02 - 7.53: 4 Bond angle restraints: 14416 Sorted by residual: angle pdb=" N3 DT C 16 " pdb=" C4 DT C 16 " pdb=" O4 DT C 16 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT D 16 " pdb=" C4 DT D 16 " pdb=" O4 DT D 16 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT C 82 " pdb=" C4 DT C 82 " pdb=" O4 DT C 82 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT D 82 " pdb=" C4 DT D 82 " pdb=" O4 DT D 82 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT D 78 " pdb=" C4 DT D 78 " pdb=" O4 DT D 78 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 14411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 5117 35.98 - 71.96: 392 71.96 - 107.93: 18 107.93 - 143.91: 8 143.91 - 179.89: 13 Dihedral angle restraints: 5548 sinusoidal: 3744 harmonic: 1804 Sorted by residual: dihedral pdb=" O4' U E 52 " pdb=" C1' U E 52 " pdb=" N1 U E 52 " pdb=" C2 U E 52 " ideal model delta sinusoidal sigma weight residual 200.00 47.39 152.61 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' C E 15 " pdb=" C1' C E 15 " pdb=" N1 C E 15 " pdb=" C2 C E 15 " ideal model delta sinusoidal sigma weight residual 200.00 48.83 151.17 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U E 68 " pdb=" C1' U E 68 " pdb=" N1 U E 68 " pdb=" C2 U E 68 " ideal model delta sinusoidal sigma weight residual -160.00 -30.80 -129.20 1 1.50e+01 4.44e-03 6.96e+01 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1265 0.039 - 0.079: 336 0.079 - 0.118: 101 0.118 - 0.157: 25 0.157 - 0.197: 4 Chirality restraints: 1731 Sorted by residual: chirality pdb=" C3' A E 66 " pdb=" C4' A E 66 " pdb=" O3' A E 66 " pdb=" C2' A E 66 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" C3' A G 66 " pdb=" C4' A G 66 " pdb=" O3' A G 66 " pdb=" C2' A G 66 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" C1' C E 65 " pdb=" O4' C E 65 " pdb=" C2' C E 65 " pdb=" N1 C E 65 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1728 not shown) Planarity restraints: 1057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 237 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 220 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO B 221 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A E 13 " 0.021 2.00e-02 2.50e+03 9.76e-03 2.62e+00 pdb=" N9 A E 13 " -0.022 2.00e-02 2.50e+03 pdb=" C8 A E 13 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A E 13 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A E 13 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A E 13 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A E 13 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A E 13 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A E 13 " -0.002 2.00e-02 2.50e+03 ... (remaining 1054 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 737 2.72 - 3.27: 8464 3.27 - 3.81: 16545 3.81 - 4.36: 20877 4.36 - 4.90: 31372 Nonbonded interactions: 77995 Sorted by model distance: nonbonded pdb=" O THR A 301 " pdb=" OG SER A 304 " model vdw 2.180 3.040 nonbonded pdb=" O ASN B 142 " pdb=" OG SER B 146 " model vdw 2.187 3.040 nonbonded pdb=" O THR B 301 " pdb=" OG SER B 304 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP A 292 " pdb=" OG SER A 295 " model vdw 2.191 3.040 nonbonded pdb=" O SER A 218 " pdb=" O2' G F 1 " model vdw 2.197 3.040 ... (remaining 77990 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 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 9 through 81) } ncs_group { reference = chain 'F' selection = chain 'H' } 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=1.00 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.090 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.005 0.043 9974 Z= 0.356 Angle : 0.686 7.531 14416 Z= 0.453 Chirality : 0.042 0.197 1731 Planarity : 0.005 0.053 1057 Dihedral : 22.509 179.890 4388 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.32), residues: 614 helix: -0.90 (0.29), residues: 308 sheet: 0.62 (0.69), residues: 62 loop : -1.46 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 297 TYR 0.011 0.001 TYR A 179 PHE 0.025 0.002 PHE B 92 TRP 0.015 0.003 TRP B 284 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.36 ( 9974) covalent geometry : angle 0.68576 / 0.45 (14416) hydrogen bonds : bond 0.12549 / 8.09 ( 389) hydrogen bonds : angle 4.88678 / 3.44 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.6634 (pttp) cc_final: 0.6325 (mtmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1289 time to fit residues: 10.4689 Evaluate side-chains 50 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0010 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.188427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.146435 restraints weight = 15102.059| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.66 r_work: 0.3702 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9974 Z= 0.140 Angle : 0.604 6.907 14416 Z= 0.325 Chirality : 0.039 0.232 1731 Planarity : 0.005 0.046 1057 Dihedral : 24.359 179.740 3146 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.36 % Allowed : 8.15 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.33), residues: 614 helix: -0.35 (0.29), residues: 312 sheet: 0.79 (0.70), residues: 62 loop : -1.38 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 297 TYR 0.016 0.001 TYR A 302 PHE 0.015 0.001 PHE B 92 TRP 0.007 0.002 TRP B 284 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 9974) covalent geometry : angle 0.60375 / 0.33 (14416) hydrogen bonds : bond 0.05168 / 3.27 ( 389) hydrogen bonds : angle 3.71781 / 2.67 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7408 (pttp) cc_final: 0.6704 (tmtt) REVERT: B 282 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7165 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.1366 time to fit residues: 9.8198 Evaluate side-chains 49 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.186106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143099 restraints weight = 14836.286| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.72 r_work: 0.3665 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9974 Z= 0.179 Angle : 0.619 6.622 14416 Z= 0.332 Chirality : 0.040 0.230 1731 Planarity : 0.005 0.049 1057 Dihedral : 24.275 179.796 3146 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.54 % Allowed : 12.32 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.33), residues: 614 helix: -0.32 (0.29), residues: 310 sheet: 0.69 (0.69), residues: 62 loop : -1.53 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.014 0.002 TYR A 302 PHE 0.016 0.002 PHE B 92 TRP 0.007 0.002 TRP A 284 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 9974) covalent geometry : angle 0.61923 / 0.33 (14416) hydrogen bonds : bond 0.05324 / 3.35 ( 389) hydrogen bonds : angle 3.69514 / 2.65 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7477 (pttp) cc_final: 0.6798 (mtmm) outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 0.1380 time to fit residues: 9.4711 Evaluate side-chains 48 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.185525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.142143 restraints weight = 15065.417| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.53 r_work: 0.3663 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9974 Z= 0.186 Angle : 0.628 6.649 14416 Z= 0.336 Chirality : 0.041 0.231 1731 Planarity : 0.005 0.051 1057 Dihedral : 24.252 179.160 3146 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.27 % Allowed : 13.77 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.32), residues: 614 helix: -0.37 (0.29), residues: 310 sheet: 0.58 (0.69), residues: 62 loop : -1.62 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.013 0.002 TYR A 302 PHE 0.016 0.002 PHE B 92 TRP 0.008 0.002 TRP B 284 HIS 0.007 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 ( 9974) covalent geometry : angle 0.62761 / 0.34 (14416) hydrogen bonds : bond 0.05334 / 3.36 ( 389) hydrogen bonds : angle 3.69457 / 2.64 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7587 (pttp) cc_final: 0.6980 (mtmm) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.1311 time to fit residues: 9.7313 Evaluate side-chains 53 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.185013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141735 restraints weight = 14789.221| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.65 r_work: 0.3647 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9974 Z= 0.181 Angle : 0.628 7.641 14416 Z= 0.334 Chirality : 0.040 0.230 1731 Planarity : 0.005 0.052 1057 Dihedral : 24.248 178.934 3146 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.81 % Allowed : 15.22 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.32), residues: 614 helix: -0.42 (0.29), residues: 310 sheet: 0.51 (0.69), residues: 62 loop : -1.61 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.010 0.002 TYR A 179 PHE 0.013 0.002 PHE B 92 TRP 0.008 0.002 TRP A 78 HIS 0.007 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 9974) covalent geometry : angle 0.62849 / 0.33 (14416) hydrogen bonds : bond 0.05262 / 3.31 ( 389) hydrogen bonds : angle 3.65388 / 2.62 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7666 (pttp) cc_final: 0.7042 (mtmm) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.1262 time to fit residues: 9.5760 Evaluate side-chains 56 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.185842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142567 restraints weight = 14954.160| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.51 r_work: 0.3671 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9974 Z= 0.170 Angle : 0.617 7.086 14416 Z= 0.329 Chirality : 0.040 0.231 1731 Planarity : 0.005 0.051 1057 Dihedral : 24.236 179.017 3146 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.54 % Allowed : 15.04 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.32), residues: 614 helix: -0.36 (0.29), residues: 310 sheet: 0.56 (0.69), residues: 62 loop : -1.60 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.011 0.002 TYR A 302 PHE 0.012 0.002 PHE B 92 TRP 0.008 0.002 TRP A 78 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 9974) covalent geometry : angle 0.61678 / 0.33 (14416) hydrogen bonds : bond 0.05142 / 3.22 ( 389) hydrogen bonds : angle 3.59356 / 2.59 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7712 (pttp) cc_final: 0.7145 (mtmm) outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.1256 time to fit residues: 10.4524 Evaluate side-chains 61 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.186713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143525 restraints weight = 15010.287| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.52 r_work: 0.3698 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9974 Z= 0.140 Angle : 0.595 6.863 14416 Z= 0.318 Chirality : 0.039 0.231 1731 Planarity : 0.005 0.048 1057 Dihedral : 24.234 179.301 3146 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.17 % Allowed : 15.76 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.33), residues: 614 helix: -0.23 (0.29), residues: 310 sheet: 0.61 (0.70), residues: 62 loop : -1.53 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 31 TYR 0.024 0.001 TYR A 302 PHE 0.011 0.001 PHE B 92 TRP 0.008 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 9974) covalent geometry : angle 0.59476 / 0.32 (14416) hydrogen bonds : bond 0.04922 / 3.07 ( 389) hydrogen bonds : angle 3.52316 / 2.54 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7676 (pttp) cc_final: 0.7043 (mtmm) outliers start: 12 outliers final: 12 residues processed: 57 average time/residue: 0.1376 time to fit residues: 10.3987 Evaluate side-chains 61 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.186135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.142719 restraints weight = 14939.773| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.52 r_work: 0.3683 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9974 Z= 0.163 Angle : 0.610 7.253 14416 Z= 0.325 Chirality : 0.040 0.232 1731 Planarity : 0.005 0.050 1057 Dihedral : 24.195 179.325 3146 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.90 % Allowed : 16.30 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.33), residues: 614 helix: -0.25 (0.29), residues: 310 sheet: 0.58 (0.69), residues: 62 loop : -1.56 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 31 TYR 0.014 0.002 TYR A 302 PHE 0.012 0.002 PHE A 10 TRP 0.007 0.002 TRP A 78 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 9974) covalent geometry : angle 0.60967 / 0.32 (14416) hydrogen bonds : bond 0.05109 / 3.19 ( 389) hydrogen bonds : angle 3.54601 / 2.55 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7689 (pttp) cc_final: 0.7117 (mtmm) outliers start: 16 outliers final: 15 residues processed: 63 average time/residue: 0.1256 time to fit residues: 10.6182 Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.186349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143052 restraints weight = 14934.094| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.52 r_work: 0.3686 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9974 Z= 0.154 Angle : 0.612 8.661 14416 Z= 0.324 Chirality : 0.039 0.232 1731 Planarity : 0.005 0.049 1057 Dihedral : 24.197 179.366 3146 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.90 % Allowed : 16.67 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.33), residues: 614 helix: -0.23 (0.29), residues: 310 sheet: 0.59 (0.69), residues: 62 loop : -1.55 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 31 TYR 0.016 0.001 TYR A 302 PHE 0.011 0.002 PHE B 92 TRP 0.008 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 9974) covalent geometry : angle 0.61231 / 0.32 (14416) hydrogen bonds : bond 0.05031 / 3.13 ( 389) hydrogen bonds : angle 3.54719 / 2.55 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7740 (pttp) cc_final: 0.7155 (mtmm) outliers start: 16 outliers final: 15 residues processed: 63 average time/residue: 0.1245 time to fit residues: 10.4383 Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.186609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.143364 restraints weight = 14939.289| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.52 r_work: 0.3694 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9974 Z= 0.145 Angle : 0.607 7.833 14416 Z= 0.321 Chirality : 0.039 0.232 1731 Planarity : 0.005 0.053 1057 Dihedral : 24.198 179.426 3146 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.72 % Allowed : 16.85 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.33), residues: 614 helix: -0.20 (0.29), residues: 310 sheet: 0.61 (0.69), residues: 62 loop : -1.53 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.014 0.001 TYR A 302 PHE 0.010 0.002 PHE B 92 TRP 0.008 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 9974) covalent geometry : angle 0.60673 / 0.32 (14416) hydrogen bonds : bond 0.04952 / 3.08 ( 389) hydrogen bonds : angle 3.51599 / 2.53 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7693 (pttp) cc_final: 0.7092 (mtmm) outliers start: 15 outliers final: 15 residues processed: 60 average time/residue: 0.1296 time to fit residues: 10.4336 Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 69 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 0.0040 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.0050 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.189216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.146722 restraints weight = 14827.467| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.51 r_work: 0.3744 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9974 Z= 0.115 Angle : 0.578 7.970 14416 Z= 0.305 Chirality : 0.037 0.231 1731 Planarity : 0.004 0.048 1057 Dihedral : 24.216 179.962 3146 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.72 % Allowed : 18.66 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.33), residues: 614 helix: -0.00 (0.29), residues: 316 sheet: 0.82 (0.70), residues: 62 loop : -1.27 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 31 TYR 0.015 0.001 TYR A 302 PHE 0.007 0.001 PHE A 92 TRP 0.011 0.002 TRP B 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.12 ( 9974) covalent geometry : angle 0.57774 / 0.31 (14416) hydrogen bonds : bond 0.04491 / 2.72 ( 389) hydrogen bonds : angle 3.33264 / 2.43 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.13 seconds wall clock time: 40 minutes 15.19 seconds (2415.19 seconds total)