Starting phenix.real_space_refine on Fri Sep 11 00:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.cif" model { file = "/net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8j_15231/09_2026/8a8j_15231.cif" } resolution = 3.1 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= -0.000 sd= 0.077 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: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 2 5.21 5 S 6 5.16 5 C 3748 2.51 5 N 1173 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 6159 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2656 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2692 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "Y" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.97, per 1000 atoms: 0.32 Number of scatterers: 6159 At special positions: 0 Unit cell: (77.4, 89.44, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 6 16.00 P 44 15.00 Mg 2 11.99 O 1186 8.00 N 1173 7.00 C 3748 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: 0.40 Conformation dependent library (CDL) restraints added in 398.9 milliseconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1238 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 46.9% alpha, 15.2% beta 12 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.636A pdb=" N ARG A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 162 Processing helix chain 'A' and resid 168 through 202 removed outlier: 3.832A pdb=" N ARG A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.880A pdb=" N ASP A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.698A pdb=" N LEU B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.936A pdb=" N GLU B 106 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.926A pdb=" N ALA B 120 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.661A pdb=" N LEU B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 163 removed outlier: 4.382A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 205 removed outlier: 3.610A pdb=" N ASP B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 4.250A pdb=" N ALA B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.642A pdb=" N ASP B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.925A pdb=" N THR B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.599A pdb=" N GLN B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 9 removed outlier: 3.623A pdb=" N LEU A 5 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.066A pdb=" N GLY A 24 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU A 319 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER A 26 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 290 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 111 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP A 293 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 113 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.511A pdb=" N ARG A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 332 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.747A pdb=" N LEU B 3 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU B 73 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 5 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 66 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.045A pdb=" N VAL B 111 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 293 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 113 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 290 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 317 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 319 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N CYS B 331 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 27 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL B 333 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 29 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 332 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 214 264 hydrogen bonds defined for protein. 713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1694 1.33 - 1.45: 1156 1.45 - 1.57: 3409 1.57 - 1.69: 84 1.69 - 1.81: 10 Bond restraints: 6353 Sorted by residual: bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O5' ANP B 901 " pdb=" PA ANP B 901 " ideal model delta sigma weight residual 1.655 1.573 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 6348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 8687 2.87 - 5.74: 69 5.74 - 8.61: 11 8.61 - 11.47: 4 11.47 - 14.34: 2 Bond angle restraints: 8773 Sorted by residual: angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 112.61 14.34 3.00e+00 1.11e-01 2.29e+01 angle pdb=" PB ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 126.95 112.74 14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" N3 DT Y 21 " pdb=" C4 DT Y 21 " pdb=" O4 DT Y 21 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT Y 8 " pdb=" C4 DT Y 8 " pdb=" O4 DT Y 8 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT X 19 " pdb=" C4 DT X 19 " pdb=" O4 DT X 19 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 8768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 3080 17.62 - 35.24: 396 35.24 - 52.86: 195 52.86 - 70.48: 31 70.48 - 88.10: 6 Dihedral angle restraints: 3708 sinusoidal: 1774 harmonic: 1934 Sorted by residual: dihedral pdb=" CG ARG A 192 " pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " ideal model delta sinusoidal sigma weight residual -180.00 -135.54 -44.46 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA GLN A 8 " pdb=" C GLN A 8 " pdb=" N ARG A 9 " pdb=" CA ARG A 9 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" N ARG B 198 " pdb=" CA BARG B 198 " pdb=" CB BARG B 198 " pdb=" CG BARG B 198 " ideal model delta sinusoidal sigma weight residual -60.00 -114.43 54.43 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 3705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 832 0.056 - 0.112: 125 0.112 - 0.169: 14 0.169 - 0.225: 0 0.225 - 0.281: 2 Chirality restraints: 973 Sorted by residual: chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU A 294 " pdb=" N GLU A 294 " pdb=" C GLU A 294 " pdb=" CB GLU A 294 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 970 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 86 " 0.039 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO B 87 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 241 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 242 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 242 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 242 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 114 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 115 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.018 5.00e-02 4.00e+02 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 25 2.59 - 3.17: 4322 3.17 - 3.74: 8502 3.74 - 4.32: 11898 4.32 - 4.90: 20269 Nonbonded interactions: 45016 Sorted by model distance: nonbonded pdb=" O2G ANP A 901 " pdb="MG MG A 902 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR B 37 " pdb="MG MG B 902 " model vdw 2.032 2.170 nonbonded pdb=" O2G ANP B 901 " pdb="MG MG B 902 " model vdw 2.048 2.170 nonbonded pdb=" O1B ANP A 901 " pdb=" O2G ANP A 901 " model vdw 2.150 3.040 nonbonded pdb=" O1B ANP B 901 " pdb=" O2G ANP B 901 " model vdw 2.155 3.040 ... (remaining 45011 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' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 197 or resid 199 through 902)) selection = (chain 'B' and (resid 1 through 197 or resid 199 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.370 Find NCS groups from input model: 0.100 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.006 0.144 6353 Z= 0.344 Angle : 0.744 14.342 8773 Z= 0.409 Chirality : 0.043 0.281 973 Planarity : 0.005 0.058 1011 Dihedral : 18.755 88.099 2470 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.19 % Allowed : 0.76 % Favored : 99.05 % 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: 0.13 (0.33), residues: 679 helix: 1.46 (0.32), residues: 275 sheet: 0.34 (0.45), residues: 138 loop : -1.55 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 223 TYR 0.009 0.001 TYR B 150 PHE 0.005 0.001 PHE A 259 TRP 0.006 0.001 TRP A 105 HIS 0.005 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.34 ( 6353) covalent geometry : angle 0.74426 / 0.41 ( 8773) hydrogen bonds : bond 0.22158 / 14.78 ( 294) hydrogen bonds : angle 6.66961 / 4.37 ( 773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1752 time to fit residues: 10.9207 Evaluate side-chains 46 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134356 restraints weight = 13425.992| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.51 r_work: 0.3361 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6353 Z= 0.134 Angle : 0.579 6.499 8773 Z= 0.301 Chirality : 0.040 0.154 973 Planarity : 0.005 0.039 1011 Dihedral : 19.512 59.619 1187 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.76 % Allowed : 4.77 % Favored : 94.47 % 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: 0.45 (0.33), residues: 679 helix: 1.69 (0.32), residues: 277 sheet: 1.10 (0.46), residues: 124 loop : -1.61 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 2 TYR 0.008 0.001 TYR B 131 PHE 0.006 0.001 PHE A 139 TRP 0.005 0.001 TRP B 171 HIS 0.005 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6353) covalent geometry : angle 0.57944 / 0.30 ( 8773) hydrogen bonds : bond 0.06175 / 4.11 ( 294) hydrogen bonds : angle 4.09626 / 2.68 ( 773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.197 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1698 time to fit residues: 10.0442 Evaluate side-chains 48 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 32 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.170828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140715 restraints weight = 9200.927| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.71 r_work: 0.3442 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6353 Z= 0.111 Angle : 0.507 5.601 8773 Z= 0.263 Chirality : 0.037 0.124 973 Planarity : 0.004 0.035 1011 Dihedral : 19.917 59.897 1187 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.95 % Allowed : 7.25 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.33), residues: 679 helix: 1.91 (0.32), residues: 277 sheet: 1.35 (0.46), residues: 124 loop : -1.55 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 188 TYR 0.007 0.001 TYR B 150 PHE 0.004 0.001 PHE A 139 TRP 0.005 0.001 TRP B 67 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 6353) covalent geometry : angle 0.50656 / 0.26 ( 8773) hydrogen bonds : bond 0.04821 / 3.17 ( 294) hydrogen bonds : angle 3.59366 / 2.35 ( 773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.205 Fit side-chains REVERT: B 229 ARG cc_start: 0.7456 (mtm110) cc_final: 0.6837 (mtt180) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1593 time to fit residues: 9.0774 Evaluate side-chains 46 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137114 restraints weight = 14691.177| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.61 r_work: 0.3363 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6353 Z= 0.133 Angle : 0.531 5.771 8773 Z= 0.273 Chirality : 0.038 0.145 973 Planarity : 0.004 0.033 1011 Dihedral : 19.847 59.822 1187 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.15 % Allowed : 10.31 % Favored : 88.55 % 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: 0.62 (0.32), residues: 679 helix: 1.86 (0.32), residues: 277 sheet: 1.29 (0.46), residues: 124 loop : -1.60 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 223 TYR 0.009 0.001 TYR B 150 PHE 0.005 0.001 PHE B 193 TRP 0.004 0.001 TRP B 171 HIS 0.006 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6353) covalent geometry : angle 0.53062 / 0.27 ( 8773) hydrogen bonds : bond 0.05107 / 3.37 ( 294) hydrogen bonds : angle 3.56339 / 2.35 ( 773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.137 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1364 time to fit residues: 7.9412 Evaluate side-chains 49 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 0.0270 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.165753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130971 restraints weight = 13462.311| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.52 r_work: 0.3321 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6353 Z= 0.189 Angle : 0.618 6.293 8773 Z= 0.311 Chirality : 0.041 0.146 973 Planarity : 0.005 0.041 1011 Dihedral : 19.933 59.613 1187 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.95 % Allowed : 11.45 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.32), residues: 679 helix: 1.61 (0.32), residues: 277 sheet: 1.11 (0.46), residues: 124 loop : -1.75 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 229 TYR 0.011 0.001 TYR B 150 PHE 0.009 0.001 PHE B 193 TRP 0.005 0.001 TRP A 105 HIS 0.009 0.002 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 6353) covalent geometry : angle 0.61828 / 0.31 ( 8773) hydrogen bonds : bond 0.06156 / 4.06 ( 294) hydrogen bonds : angle 3.68420 / 2.45 ( 773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.266 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.1512 time to fit residues: 9.2560 Evaluate side-chains 49 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.0000 chunk 41 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139052 restraints weight = 10740.915| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.15 r_work: 0.3411 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6353 Z= 0.104 Angle : 0.496 5.790 8773 Z= 0.260 Chirality : 0.036 0.139 973 Planarity : 0.004 0.035 1011 Dihedral : 19.906 59.552 1187 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.15 % Allowed : 11.83 % Favored : 87.02 % 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: 0.63 (0.32), residues: 679 helix: 1.90 (0.32), residues: 277 sheet: 1.35 (0.46), residues: 124 loop : -1.66 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 188 TYR 0.007 0.001 TYR B 150 PHE 0.004 0.000 PHE A 139 TRP 0.007 0.001 TRP B 67 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 6353) covalent geometry : angle 0.49638 / 0.26 ( 8773) hydrogen bonds : bond 0.04441 / 2.90 ( 294) hydrogen bonds : angle 3.48776 / 2.30 ( 773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.224 Fit side-chains REVERT: B 122 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8398 (pp) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.1600 time to fit residues: 9.1858 Evaluate side-chains 46 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134458 restraints weight = 13350.440| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.51 r_work: 0.3365 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6353 Z= 0.120 Angle : 0.515 6.599 8773 Z= 0.264 Chirality : 0.037 0.135 973 Planarity : 0.004 0.039 1011 Dihedral : 19.855 59.525 1187 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.15 % Allowed : 12.02 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.32), residues: 679 helix: 1.92 (0.32), residues: 277 sheet: 1.36 (0.46), residues: 124 loop : -1.65 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 223 TYR 0.009 0.001 TYR B 150 PHE 0.004 0.001 PHE A 139 TRP 0.004 0.001 TRP B 171 HIS 0.005 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6353) covalent geometry : angle 0.51489 / 0.26 ( 8773) hydrogen bonds : bond 0.04705 / 3.09 ( 294) hydrogen bonds : angle 3.42458 / 2.27 ( 773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.213 Fit side-chains REVERT: B 122 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8425 (pp) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1511 time to fit residues: 8.8248 Evaluate side-chains 46 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 40 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138051 restraints weight = 8878.287| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.94 r_work: 0.3427 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6353 Z= 0.112 Angle : 0.502 5.927 8773 Z= 0.259 Chirality : 0.036 0.146 973 Planarity : 0.004 0.034 1011 Dihedral : 19.856 59.783 1187 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.53 % Allowed : 11.64 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.32), residues: 679 helix: 1.95 (0.32), residues: 279 sheet: 1.39 (0.46), residues: 124 loop : -1.62 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 223 TYR 0.008 0.001 TYR B 150 PHE 0.004 0.001 PHE A 139 TRP 0.005 0.001 TRP B 171 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6353) covalent geometry : angle 0.50242 / 0.26 ( 8773) hydrogen bonds : bond 0.04461 / 2.92 ( 294) hydrogen bonds : angle 3.38603 / 2.25 ( 773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.205 Fit side-chains REVERT: B 122 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8431 (pp) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.1541 time to fit residues: 8.3478 Evaluate side-chains 44 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.0040 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137447 restraints weight = 10730.763| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.19 r_work: 0.3409 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6353 Z= 0.107 Angle : 0.495 6.626 8773 Z= 0.256 Chirality : 0.036 0.157 973 Planarity : 0.004 0.034 1011 Dihedral : 19.828 59.200 1187 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.15 % Allowed : 12.40 % Favored : 86.45 % 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: 0.81 (0.33), residues: 679 helix: 2.04 (0.32), residues: 279 sheet: 1.13 (0.44), residues: 134 loop : -1.50 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 223 TYR 0.008 0.001 TYR B 150 PHE 0.003 0.001 PHE A 139 TRP 0.005 0.001 TRP B 171 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 6353) covalent geometry : angle 0.49513 / 0.26 ( 8773) hydrogen bonds : bond 0.04216 / 2.76 ( 294) hydrogen bonds : angle 3.30956 / 2.20 ( 773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.266 Fit side-chains REVERT: B 122 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8399 (pp) REVERT: B 229 ARG cc_start: 0.7408 (mtm110) cc_final: 0.6868 (mtt180) REVERT: B 339 LEU cc_start: 0.7749 (pt) cc_final: 0.7224 (tp) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.1705 time to fit residues: 8.4258 Evaluate side-chains 43 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134101 restraints weight = 14646.764| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.65 r_work: 0.3357 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6353 Z= 0.123 Angle : 0.515 5.922 8773 Z= 0.264 Chirality : 0.037 0.141 973 Planarity : 0.004 0.040 1011 Dihedral : 19.819 59.471 1187 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.15 % Allowed : 12.40 % Favored : 86.45 % 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: 0.76 (0.32), residues: 679 helix: 1.98 (0.32), residues: 279 sheet: 1.38 (0.46), residues: 124 loop : -1.57 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 223 TYR 0.008 0.001 TYR B 150 PHE 0.004 0.001 PHE A 139 TRP 0.004 0.001 TRP A 105 HIS 0.005 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6353) covalent geometry : angle 0.51532 / 0.26 ( 8773) hydrogen bonds : bond 0.04555 / 2.99 ( 294) hydrogen bonds : angle 3.32543 / 2.21 ( 773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.128 Fit side-chains REVERT: A 106 GLU cc_start: 0.6223 (tm-30) cc_final: 0.5974 (tp30) REVERT: B 122 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8405 (pp) REVERT: B 229 ARG cc_start: 0.7415 (mtm110) cc_final: 0.6827 (mtt180) REVERT: B 339 LEU cc_start: 0.7802 (pt) cc_final: 0.7263 (tp) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.1600 time to fit residues: 8.1847 Evaluate side-chains 42 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.171231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141025 restraints weight = 6997.667| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.66 r_work: 0.3472 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6353 Z= 0.103 Angle : 0.484 5.800 8773 Z= 0.251 Chirality : 0.036 0.139 973 Planarity : 0.004 0.042 1011 Dihedral : 19.817 59.315 1187 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.34 % Allowed : 12.40 % Favored : 86.26 % 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: 0.93 (0.33), residues: 679 helix: 2.10 (0.32), residues: 279 sheet: 1.25 (0.44), residues: 134 loop : -1.43 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 223 TYR 0.008 0.001 TYR B 150 PHE 0.005 0.001 PHE B 11 TRP 0.006 0.001 TRP B 171 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6353) covalent geometry : angle 0.48444 / 0.25 ( 8773) hydrogen bonds : bond 0.04039 / 2.64 ( 294) hydrogen bonds : angle 3.26806 / 2.18 ( 773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.34 seconds wall clock time: 29 minutes 27.34 seconds (1767.34 seconds total)