Starting phenix.real_space_refine on Fri Sep 11 17:21:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9x_31829/09_2026/7v9x_31829.map" } resolution = 2.82 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= 0.005 sd= 0.071 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 210 5.49 5 S 23 5.16 5 C 5946 2.51 5 N 1901 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10550 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "C" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 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: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNAv2': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" 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: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNAv2': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Time building chain proxies: 2.37, per 1000 atoms: 0.22 Number of scatterers: 10550 At special positions: 0 Unit cell: (94.35, 129.2, 155.55, 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 23 16.00 P 210 15.00 O 2470 8.00 N 1901 7.00 C 5946 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: 0.90 Conformation dependent library (CDL) restraints added in 232.9 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 60.5% alpha, 10.9% beta 64 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 removed outlier: 3.633A pdb=" N LEU A 7 " --> pdb=" O SER A 3 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.581A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.733A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix 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 122 through 127 removed outlier: 3.691A pdb=" N LEU A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.756A pdb=" N VAL A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 188 removed outlier: 4.625A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.606A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.655A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.766A pdb=" N GLN C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.575A pdb=" N ARG C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.937A pdb=" N ASN B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 33 through 43 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.615A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 102 through 107 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 123 through 127 Processing helix chain 'B' and resid 128 through 139 removed outlier: 4.060A pdb=" N VAL B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.838A 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 Processing helix chain 'B' and resid 175 through 188 removed outlier: 4.232A pdb=" N SER B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.664A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 256 through 273 removed outlier: 3.619A pdb=" N TYR B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.679A pdb=" N LYS B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 3.643A 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 242 through 243 Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.979A pdb=" N ARG B 63 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.543A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.543A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 332 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 161 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.21 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: 1841 1.33 - 1.45: 3746 1.45 - 1.57: 5159 1.57 - 1.69: 410 1.69 - 1.81: 34 Bond restraints: 11190 Sorted by residual: bond pdb=" C3' DT G 17 " pdb=" C2' DT G 17 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT D 17 " pdb=" C2' DT D 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.32e+00 bond pdb=" C1' DC D 75 " pdb=" N1 DC D 75 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.25e+00 bond pdb=" C3' DA D 10 " pdb=" C2' DA D 10 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.69e+00 bond pdb=" C3' DC D 75 " pdb=" C2' DC D 75 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.11e+00 ... (remaining 11185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 15306 2.10 - 4.20: 657 4.20 - 6.30: 83 6.30 - 8.40: 4 8.40 - 10.50: 1 Bond angle restraints: 16051 Sorted by residual: angle pdb=" O4' DT D 82 " pdb=" C4' DT D 82 " pdb=" C3' DT D 82 " ideal model delta sigma weight residual 106.00 102.75 3.25 6.00e-01 2.78e+00 2.94e+01 angle pdb=" O4' DC D 83 " pdb=" C4' DC D 83 " pdb=" C3' DC D 83 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.44e+01 angle pdb=" C3' A E 66 " pdb=" O3' A E 66 " pdb=" P U E 67 " ideal model delta sigma weight residual 119.70 125.43 -5.73 1.20e+00 6.94e-01 2.28e+01 angle pdb=" O4' DC G 83 " pdb=" C4' DC G 83 " pdb=" C3' DC G 83 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.28e+01 angle pdb=" O4' DG G 85 " pdb=" C4' DG G 85 " pdb=" C3' DG G 85 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 16046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 5645 34.36 - 68.72: 613 68.72 - 103.08: 34 103.08 - 137.44: 1 137.44 - 171.80: 5 Dihedral angle restraints: 6298 sinusoidal: 4073 harmonic: 2225 Sorted by residual: dihedral pdb=" C4' C E 39 " pdb=" C3' C E 39 " pdb=" C2' C E 39 " pdb=" C1' C E 39 " ideal model delta sinusoidal sigma weight residual 36.35 -37.78 74.12 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' C H 39 " pdb=" C3' C H 39 " pdb=" C2' C H 39 " pdb=" C1' C H 39 " ideal model delta sinusoidal sigma weight residual 36.34 -37.75 74.09 1 3.10e+00 1.04e-01 7.25e+02 dihedral pdb=" C4' C E 40 " pdb=" C3' C E 40 " pdb=" C2' C E 40 " pdb=" C1' C E 40 " ideal model delta sinusoidal sigma weight residual 36.34 -37.40 73.75 1 3.10e+00 1.04e-01 7.19e+02 ... (remaining 6295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1537 0.071 - 0.143: 176 0.143 - 0.214: 36 0.214 - 0.285: 155 0.285 - 0.357: 12 Chirality restraints: 1916 Sorted by residual: chirality pdb=" P C E 9 " pdb=" OP1 C E 9 " pdb=" OP2 C E 9 " pdb=" O5' C E 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" P C H 9 " pdb=" OP1 C H 9 " pdb=" OP2 C H 9 " pdb=" O5' C H 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" P U H 67 " pdb=" OP1 U H 67 " pdb=" OP2 U H 67 " pdb=" O5' U H 67 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 1913 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A E 17 " -0.023 2.00e-02 2.50e+03 1.08e-02 3.19e+00 pdb=" N9 A E 17 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A E 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A E 17 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A E 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A E 17 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A E 17 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A E 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A E 17 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A E 17 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A E 17 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 80 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LEU B 80 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU B 80 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 81 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 6 " -0.018 2.00e-02 2.50e+03 8.09e-03 1.80e+00 pdb=" N9 DA D 6 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA D 6 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA D 6 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA D 6 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA D 6 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA D 6 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA D 6 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA D 6 " 0.002 2.00e-02 2.50e+03 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1933 2.77 - 3.30: 8918 3.30 - 3.84: 18963 3.84 - 4.37: 23081 4.37 - 4.90: 35214 Nonbonded interactions: 88109 Sorted by model distance: nonbonded pdb=" OD1 ASN B 8 " pdb=" NH2 ARG B 11 " model vdw 2.241 3.120 nonbonded pdb=" O TYR C 211 " pdb=" NH2 ARG B 31 " model vdw 2.254 3.120 nonbonded pdb=" O LEU A 39 " pdb=" OG1 THR A 43 " model vdw 2.260 3.040 nonbonded pdb=" NZ LYS B 60 " pdb=" OE2 GLU B 121 " model vdw 2.274 3.120 nonbonded pdb=" O PHE B 287 " pdb=" OG SER B 290 " model vdw 2.276 3.040 ... (remaining 88104 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 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } 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: 1.550 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.320 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 0.040 11190 Z= 0.359 Angle : 0.866 10.501 16051 Z= 0.496 Chirality : 0.088 0.357 1916 Planarity : 0.004 0.045 1259 Dihedral : 22.353 171.795 4864 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.30), residues: 750 helix: 0.89 (0.27), residues: 394 sheet: 1.50 (0.64), residues: 62 loop : -1.26 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.013 0.001 TYR B 179 PHE 0.013 0.002 PHE B 92 TRP 0.007 0.002 TRP B 284 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.36 (11190) covalent geometry : angle 0.86586 / 0.50 (16051) hydrogen bonds : bond 0.12453 / 8.38 ( 484) hydrogen bonds : angle 4.54192 / 3.17 ( 1238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.281 Fit side-chains REVERT: A 45 ASP cc_start: 0.7618 (m-30) cc_final: 0.7343 (m-30) REVERT: A 231 LYS cc_start: 0.6377 (mptt) cc_final: 0.6076 (mptt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.6216 time to fit residues: 59.3123 Evaluate side-chains 63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN B 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.147651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100090 restraints weight = 14805.344| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.70 r_work: 0.3174 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11190 Z= 0.260 Angle : 1.358 20.531 16051 Z= 0.556 Chirality : 0.142 1.354 1916 Planarity : 0.005 0.039 1259 Dihedral : 22.718 178.368 3317 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.32 % Allowed : 7.92 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.30), residues: 750 helix: 0.93 (0.26), residues: 400 sheet: 2.01 (0.62), residues: 58 loop : -1.46 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 246 TYR 0.013 0.001 TYR B 179 PHE 0.014 0.002 PHE B 92 TRP 0.008 0.002 TRP B 284 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (11190) covalent geometry : angle 1.35810 / 0.56 (16051) hydrogen bonds : bond 0.05769 / 3.73 ( 484) hydrogen bonds : angle 3.85051 / 2.69 ( 1238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8032 (m-30) cc_final: 0.7642 (m-30) REVERT: A 62 MET cc_start: 0.7397 (pmm) cc_final: 0.6623 (ppp) REVERT: A 119 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8433 (m-30) REVERT: A 231 LYS cc_start: 0.6139 (mptt) cc_final: 0.5862 (mptt) REVERT: C 239 ILE cc_start: 0.7911 (mp) cc_final: 0.7708 (tt) REVERT: B 251 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7607 (mm-30) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.6211 time to fit residues: 46.1726 Evaluate side-chains 72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 36 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN B 240 GLN B 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103928 restraints weight = 14905.785| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.68 r_work: 0.3224 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11190 Z= 0.173 Angle : 1.024 14.969 16051 Z= 0.434 Chirality : 0.094 0.887 1916 Planarity : 0.004 0.031 1259 Dihedral : 23.038 173.059 3317 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.32 % Allowed : 9.24 % Favored : 89.44 % 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: 0.50 (0.30), residues: 750 helix: 1.25 (0.27), residues: 399 sheet: 2.14 (0.63), residues: 58 loop : -1.36 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 246 TYR 0.009 0.001 TYR B 179 PHE 0.013 0.001 PHE B 92 TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (11190) covalent geometry : angle 1.02375 / 0.43 (16051) hydrogen bonds : bond 0.04703 / 3.05 ( 484) hydrogen bonds : angle 3.54662 / 2.49 ( 1238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7930 (m-30) cc_final: 0.7664 (m-30) REVERT: A 62 MET cc_start: 0.7395 (pmm) cc_final: 0.6671 (ppp) REVERT: A 119 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: A 231 LYS cc_start: 0.6036 (mptt) cc_final: 0.5633 (mptt) REVERT: B 251 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: B 282 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7830 (ttp-170) outliers start: 9 outliers final: 3 residues processed: 72 average time/residue: 0.6001 time to fit residues: 46.5960 Evaluate side-chains 72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098328 restraints weight = 14830.629| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.69 r_work: 0.3124 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11190 Z= 0.285 Angle : 1.064 13.295 16051 Z= 0.466 Chirality : 0.093 0.924 1916 Planarity : 0.005 0.047 1259 Dihedral : 23.004 177.954 3317 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.05 % Allowed : 11.00 % Favored : 86.95 % 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: 0.10 (0.30), residues: 750 helix: 0.95 (0.26), residues: 396 sheet: 1.79 (0.61), residues: 58 loop : -1.55 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.017 0.002 TYR B 179 PHE 0.013 0.002 PHE B 10 TRP 0.007 0.002 TRP B 284 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.28 (11190) covalent geometry : angle 1.06372 / 0.47 (16051) hydrogen bonds : bond 0.06386 / 4.12 ( 484) hydrogen bonds : angle 3.79094 / 2.69 ( 1238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7959 (m-30) cc_final: 0.7673 (m-30) REVERT: A 119 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: A 231 LYS cc_start: 0.6162 (mptt) cc_final: 0.5876 (mptt) REVERT: C 241 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7252 (tpm-80) REVERT: B 251 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: B 282 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7862 (ttp-170) outliers start: 14 outliers final: 8 residues processed: 71 average time/residue: 0.5617 time to fit residues: 43.0550 Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.149708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102307 restraints weight = 14802.241| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.69 r_work: 0.3201 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11190 Z= 0.166 Angle : 0.950 12.615 16051 Z= 0.411 Chirality : 0.083 0.895 1916 Planarity : 0.004 0.033 1259 Dihedral : 23.094 176.379 3317 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.61 % Allowed : 11.88 % Favored : 86.51 % 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: 0.32 (0.30), residues: 750 helix: 1.14 (0.26), residues: 398 sheet: 2.01 (0.62), residues: 58 loop : -1.50 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 246 TYR 0.010 0.001 TYR B 179 PHE 0.013 0.001 PHE B 92 TRP 0.006 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (11190) covalent geometry : angle 0.95043 / 0.41 (16051) hydrogen bonds : bond 0.04758 / 3.07 ( 484) hydrogen bonds : angle 3.54189 / 2.50 ( 1238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7924 (m-30) cc_final: 0.7613 (m-30) REVERT: A 119 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: A 231 LYS cc_start: 0.6093 (mptt) cc_final: 0.5785 (mptt) REVERT: C 241 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7220 (tpm-80) REVERT: B 251 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: B 282 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7860 (ttp-170) outliers start: 11 outliers final: 4 residues processed: 70 average time/residue: 0.5803 time to fit residues: 43.9395 Evaluate side-chains 72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 57 optimal weight: 0.0270 chunk 88 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104919 restraints weight = 14869.278| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.62 r_work: 0.3259 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11190 Z= 0.147 Angle : 0.891 12.955 16051 Z= 0.384 Chirality : 0.077 0.841 1916 Planarity : 0.003 0.030 1259 Dihedral : 22.991 177.843 3317 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.61 % Allowed : 12.46 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.31), residues: 750 helix: 1.50 (0.27), residues: 399 sheet: 1.05 (0.63), residues: 72 loop : -1.23 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 246 TYR 0.008 0.001 TYR B 179 PHE 0.010 0.001 PHE C 226 TRP 0.006 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (11190) covalent geometry : angle 0.89108 / 0.38 (16051) hydrogen bonds : bond 0.04363 / 2.79 ( 484) hydrogen bonds : angle 3.29878 / 2.34 ( 1238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7816 (m-30) cc_final: 0.7569 (m-30) REVERT: A 62 MET cc_start: 0.7374 (pmm) cc_final: 0.6673 (ppp) REVERT: A 119 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: A 207 LYS cc_start: 0.8192 (ptmm) cc_final: 0.7901 (pttp) REVERT: A 231 LYS cc_start: 0.5961 (mptt) cc_final: 0.5542 (mptt) REVERT: B 251 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: B 282 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7820 (ttp-170) outliers start: 11 outliers final: 4 residues processed: 77 average time/residue: 0.5809 time to fit residues: 48.4320 Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 5 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.151923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104259 restraints weight = 14756.021| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.67 r_work: 0.3222 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11190 Z= 0.151 Angle : 0.888 12.996 16051 Z= 0.384 Chirality : 0.077 0.823 1916 Planarity : 0.004 0.037 1259 Dihedral : 22.933 178.287 3317 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.61 % Allowed : 12.76 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.31), residues: 750 helix: 1.48 (0.27), residues: 399 sheet: 1.02 (0.62), residues: 72 loop : -1.21 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 246 TYR 0.009 0.001 TYR B 179 PHE 0.012 0.001 PHE B 92 TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (11190) covalent geometry : angle 0.88800 / 0.38 (16051) hydrogen bonds : bond 0.04434 / 2.84 ( 484) hydrogen bonds : angle 3.31668 / 2.36 ( 1238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7827 (m-30) cc_final: 0.7595 (m-30) REVERT: A 62 MET cc_start: 0.7380 (pmm) cc_final: 0.5848 (ttp) REVERT: A 119 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: A 207 LYS cc_start: 0.8208 (ptmm) cc_final: 0.7908 (pttp) REVERT: A 231 LYS cc_start: 0.5995 (mptt) cc_final: 0.5583 (mptt) REVERT: B 251 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: B 282 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7826 (ttp-170) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.5903 time to fit residues: 45.1540 Evaluate side-chains 72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 75 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.147469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099449 restraints weight = 14662.923| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.69 r_work: 0.3151 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11190 Z= 0.238 Angle : 0.963 13.062 16051 Z= 0.425 Chirality : 0.082 0.848 1916 Planarity : 0.005 0.041 1259 Dihedral : 22.953 179.879 3317 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.61 % Allowed : 13.20 % Favored : 85.19 % 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: 0.40 (0.30), residues: 750 helix: 1.22 (0.26), residues: 400 sheet: 1.20 (0.58), residues: 68 loop : -1.40 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 70 TYR 0.017 0.002 TYR B 179 PHE 0.014 0.002 PHE B 92 TRP 0.006 0.002 TRP B 284 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (11190) covalent geometry : angle 0.96298 / 0.43 (16051) hydrogen bonds : bond 0.05872 / 3.77 ( 484) hydrogen bonds : angle 3.54815 / 2.53 ( 1238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7899 (m-30) cc_final: 0.7646 (m-30) REVERT: A 119 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: A 207 LYS cc_start: 0.8294 (ptmm) cc_final: 0.7968 (pttp) REVERT: A 231 LYS cc_start: 0.6143 (mptt) cc_final: 0.5690 (mptt) REVERT: B 251 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: B 282 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7847 (ttp-170) outliers start: 11 outliers final: 5 residues processed: 69 average time/residue: 0.6242 time to fit residues: 46.3276 Evaluate side-chains 70 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.149264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101466 restraints weight = 14725.503| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.68 r_work: 0.3184 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11190 Z= 0.161 Angle : 0.917 12.618 16051 Z= 0.401 Chirality : 0.079 0.831 1916 Planarity : 0.004 0.035 1259 Dihedral : 22.992 178.812 3317 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.47 % Allowed : 13.34 % Favored : 85.19 % 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: 0.56 (0.31), residues: 750 helix: 1.38 (0.27), residues: 400 sheet: 1.23 (0.58), residues: 68 loop : -1.36 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 246 TYR 0.013 0.001 TYR B 179 PHE 0.013 0.001 PHE B 92 TRP 0.005 0.001 TRP B 284 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (11190) covalent geometry : angle 0.91727 / 0.40 (16051) hydrogen bonds : bond 0.04947 / 3.17 ( 484) hydrogen bonds : angle 3.43936 / 2.45 ( 1238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7874 (m-30) cc_final: 0.7604 (m-30) REVERT: A 62 MET cc_start: 0.7415 (pmm) cc_final: 0.5755 (ttp) REVERT: A 119 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: A 207 LYS cc_start: 0.8250 (ptmm) cc_final: 0.7943 (pttp) REVERT: A 231 LYS cc_start: 0.6113 (mptt) cc_final: 0.5800 (mptt) REVERT: B 251 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: B 282 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7897 (ttp-170) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.5724 time to fit residues: 43.2946 Evaluate side-chains 73 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.146429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098780 restraints weight = 14608.804| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.67 r_work: 0.3133 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11190 Z= 0.270 Angle : 0.994 12.588 16051 Z= 0.441 Chirality : 0.085 0.852 1916 Planarity : 0.005 0.045 1259 Dihedral : 23.030 179.645 3317 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.76 % Allowed : 12.90 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.30), residues: 750 helix: 1.04 (0.26), residues: 396 sheet: 0.99 (0.58), residues: 68 loop : -1.55 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 70 TYR 0.018 0.002 TYR B 179 PHE 0.014 0.002 PHE B 92 TRP 0.006 0.002 TRP B 284 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 (11190) covalent geometry : angle 0.99442 / 0.44 (16051) hydrogen bonds : bond 0.06244 / 4.00 ( 484) hydrogen bonds : angle 3.66103 / 2.62 ( 1238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7944 (m-30) cc_final: 0.7682 (m-30) REVERT: A 119 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: B 251 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: B 282 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7905 (ttp-170) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.5773 time to fit residues: 45.5177 Evaluate side-chains 74 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 46 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.149211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101564 restraints weight = 14742.826| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.68 r_work: 0.3183 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11190 Z= 0.159 Angle : 0.922 11.816 16051 Z= 0.404 Chirality : 0.080 0.833 1916 Planarity : 0.004 0.035 1259 Dihedral : 23.068 178.758 3317 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.32 % Allowed : 13.78 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.30), residues: 750 helix: 1.24 (0.27), residues: 398 sheet: 1.84 (0.61), residues: 58 loop : -1.49 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 246 TYR 0.012 0.001 TYR B 179 PHE 0.014 0.001 PHE B 92 TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (11190) covalent geometry : angle 0.92244 / 0.40 (16051) hydrogen bonds : bond 0.04926 / 3.17 ( 484) hydrogen bonds : angle 3.46461 / 2.47 ( 1238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.75 seconds wall clock time: 66 minutes 37.00 seconds (3997.00 seconds total)