Starting phenix.real_space_refine on Thu Jul 2 03:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a8j_15231/07_2026/8a8j_15231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8j_15231/07_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_15231/07_2026/8a8j_15231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8j_15231/07_2026/8a8j_15231.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8a8j_15231/07_2026/8a8j_15231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a8j_15231/07_2026/8a8j_15231.cif" model { file = "/net/cci-nas-00/data/ceres_data/8a8j_15231/07_2026/8a8j_15231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8j_15231/07_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-dev-6108/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: 1.85, per 1000 atoms: 0.30 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: 0.55 Conformation dependent library (CDL) restraints added in 536.6 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: 0.68 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: 1.13 Time building geometry restraints manager: 0.72 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: 3.260 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.420 Find NCS groups from input model: 0.110 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.270 ------------------------------------------------------------------------------- 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 : 0.743 14.342 8773 Z= 0.407 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 0.74314 / 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 : 0.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1494 time to fit residues: 9.3729 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 : 0.232 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.168562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134534 restraints weight = 13428.315| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.50 r_work: 0.3347 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- 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: 0.8420 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6353 Z= 0.132 Angle : 0.582 6.803 8773 Z= 0.300 Chirality : 0.040 0.176 973 Planarity : 0.005 0.040 1011 Dihedral : 19.599 59.999 1187 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.76 % Allowed : 4.96 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.33), residues: 679 helix: 1.67 (0.32), residues: 277 sheet: 1.09 (0.46), residues: 124 loop : -1.61 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 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 0.00273 / 0.13 ( 6353) covalent geometry : angle 0.58195 / 0.30 ( 8773) hydrogen bonds : bond 0.06029 / 3.98 ( 294) hydrogen bonds : angle 4.06346 / 2.66 ( 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 : 0.262 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1495 time to fit residues: 9.0070 Evaluate side-chains 47 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 32 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.170084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139933 restraints weight = 9212.312| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.71 r_work: 0.3434 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6353 Z= 0.114 Angle : 0.511 5.595 8773 Z= 0.266 Chirality : 0.037 0.126 973 Planarity : 0.004 0.034 1011 Dihedral : 19.858 59.743 1187 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.95 % Allowed : 7.44 % Favored : 91.60 % 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: 0.67 (0.33), residues: 679 helix: 1.90 (0.32), residues: 277 sheet: 1.29 (0.46), residues: 124 loop : -1.56 (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 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 6353) covalent geometry : angle 0.51064 / 0.27 ( 8773) hydrogen bonds : bond 0.05079 / 3.35 ( 294) hydrogen bonds : angle 3.64422 / 2.39 ( 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 50 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.201 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.1340 time to fit residues: 7.8952 Evaluate side-chains 47 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 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: 0.9980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.168390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135181 restraints weight = 14726.595| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.48 r_work: 0.3347 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6353 Z= 0.165 Angle : 0.578 6.084 8773 Z= 0.294 Chirality : 0.040 0.154 973 Planarity : 0.005 0.037 1011 Dihedral : 19.901 59.861 1187 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.34 % Allowed : 9.92 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.32), residues: 679 helix: 1.70 (0.32), residues: 277 sheet: 1.18 (0.46), residues: 124 loop : -1.69 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 223 TYR 0.010 0.001 TYR B 150 PHE 0.007 0.001 PHE B 193 TRP 0.003 0.001 TRP B 171 HIS 0.008 0.002 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6353) covalent geometry : angle 0.57754 / 0.29 ( 8773) hydrogen bonds : bond 0.05734 / 3.78 ( 294) hydrogen bonds : angle 3.65577 / 2.42 ( 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 53 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.225 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.1405 time to fit residues: 8.5514 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 : 0.200 ------------------------------------------------------------------------------- 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 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.0010 chunk 23 optimal weight: 0.0670 overall best weight: 0.7824 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.168595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133956 restraints weight = 13415.195| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.51 r_work: 0.3368 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6353 Z= 0.124 Angle : 0.516 5.879 8773 Z= 0.267 Chirality : 0.038 0.135 973 Planarity : 0.004 0.035 1011 Dihedral : 19.916 59.625 1187 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.95 % Allowed : 11.26 % Favored : 87.79 % 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: 0.57 (0.32), residues: 679 helix: 1.84 (0.32), residues: 277 sheet: 1.27 (0.46), residues: 124 loop : -1.67 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.008 0.001 TYR B 150 PHE 0.005 0.001 PHE A 139 TRP 0.005 0.001 TRP B 171 HIS 0.005 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6353) covalent geometry : angle 0.51564 / 0.27 ( 8773) hydrogen bonds : bond 0.04986 / 3.27 ( 294) hydrogen bonds : angle 3.53830 / 2.34 ( 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 51 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.197 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.1567 time to fit residues: 9.2732 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 : 0.204 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 66 optimal weight: 0.0010 chunk 31 optimal weight: 0.0370 chunk 7 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.1464 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.173299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140563 restraints weight = 10695.027| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.19 r_work: 0.3446 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6353 Z= 0.096 Angle : 0.464 5.279 8773 Z= 0.244 Chirality : 0.035 0.140 973 Planarity : 0.004 0.035 1011 Dihedral : 19.856 59.512 1187 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.95 % Allowed : 12.02 % 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: 0.82 (0.33), residues: 679 helix: 2.01 (0.32), residues: 279 sheet: 1.19 (0.44), residues: 134 loop : -1.49 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 188 TYR 0.006 0.001 TYR B 150 PHE 0.003 0.000 PHE B 193 TRP 0.008 0.001 TRP B 67 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.10 ( 6353) covalent geometry : angle 0.46424 / 0.24 ( 8773) hydrogen bonds : bond 0.03788 / 2.48 ( 294) hydrogen bonds : angle 3.35371 / 2.21 ( 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 48 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.213 Fit side-chains REVERT: B 229 ARG cc_start: 0.7372 (mtm110) cc_final: 0.6896 (mtt180) REVERT: B 339 LEU cc_start: 0.7694 (pt) cc_final: 0.7154 (tp) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1528 time to fit residues: 8.5655 Evaluate side-chains 42 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.0570 chunk 40 optimal weight: 0.0670 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137390 restraints weight = 13338.021| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.52 r_work: 0.3411 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6353 Z= 0.102 Angle : 0.467 5.258 8773 Z= 0.244 Chirality : 0.036 0.133 973 Planarity : 0.004 0.032 1011 Dihedral : 19.807 59.768 1187 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.95 % Allowed : 12.60 % 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: 0.92 (0.33), residues: 679 helix: 2.12 (0.32), residues: 277 sheet: 1.23 (0.44), residues: 134 loop : -1.43 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 229 TYR 0.007 0.001 TYR B 150 PHE 0.005 0.001 PHE A 139 TRP 0.004 0.001 TRP B 67 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 6353) covalent geometry : angle 0.46676 / 0.24 ( 8773) hydrogen bonds : bond 0.03989 / 2.62 ( 294) hydrogen bonds : angle 3.28429 / 2.17 ( 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 46 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.253 Fit side-chains REVERT: B 229 ARG cc_start: 0.7386 (mtm110) cc_final: 0.6862 (mtt180) REVERT: B 339 LEU cc_start: 0.7733 (pt) cc_final: 0.7192 (tp) outliers start: 4 outliers final: 4 residues processed: 45 average time/residue: 0.1410 time to fit residues: 7.8145 Evaluate side-chains 44 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 0.0270 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.0030 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4648 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.172242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140499 restraints weight = 8892.646| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3453 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6353 Z= 0.101 Angle : 0.468 5.516 8773 Z= 0.244 Chirality : 0.036 0.139 973 Planarity : 0.004 0.032 1011 Dihedral : 19.799 59.725 1187 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.15 % Allowed : 12.21 % Favored : 86.64 % 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: 0.98 (0.33), residues: 679 helix: 2.16 (0.32), residues: 277 sheet: 1.25 (0.44), residues: 134 loop : -1.38 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 229 TYR 0.007 0.001 TYR B 150 PHE 0.004 0.001 PHE A 139 TRP 0.004 0.001 TRP B 67 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 6353) covalent geometry : angle 0.46809 / 0.24 ( 8773) hydrogen bonds : bond 0.03941 / 2.59 ( 294) hydrogen bonds : angle 3.25770 / 2.16 ( 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 46 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.174 Fit side-chains REVERT: B 229 ARG cc_start: 0.7329 (mtm110) cc_final: 0.6781 (mtt180) REVERT: B 339 LEU cc_start: 0.7739 (pt) cc_final: 0.7191 (tp) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.1447 time to fit residues: 7.8443 Evaluate side-chains 43 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 0.0170 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.171319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138145 restraints weight = 10738.524| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.19 r_work: 0.3403 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 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: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6353 Z= 0.111 Angle : 0.482 5.247 8773 Z= 0.250 Chirality : 0.036 0.136 973 Planarity : 0.004 0.031 1011 Dihedral : 19.795 59.911 1187 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.15 % Allowed : 12.21 % Favored : 86.64 % 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: 0.99 (0.33), residues: 679 helix: 2.16 (0.32), residues: 277 sheet: 1.23 (0.44), residues: 134 loop : -1.35 (0.36), residues: 268 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 0.005 0.001 PHE A 139 TRP 0.006 0.001 TRP B 105 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6353) covalent geometry : angle 0.48193 / 0.25 ( 8773) hydrogen bonds : bond 0.04156 / 2.73 ( 294) hydrogen bonds : angle 3.25915 / 2.16 ( 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 45 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.166 Fit side-chains REVERT: B 229 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6877 (mtt180) REVERT: B 339 LEU cc_start: 0.7731 (pt) cc_final: 0.7193 (tp) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.1249 time to fit residues: 6.7302 Evaluate side-chains 43 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 0.0070 chunk 14 optimal weight: 0.2980 overall best weight: 0.2096 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.174269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140703 restraints weight = 14653.933| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.52 r_work: 0.3404 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1564 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= 0.092 Angle : 0.455 6.359 8773 Z= 0.238 Chirality : 0.035 0.146 973 Planarity : 0.004 0.034 1011 Dihedral : 19.781 59.170 1187 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.95 % Allowed : 12.40 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.33), residues: 679 helix: 2.42 (0.32), residues: 273 sheet: 1.40 (0.44), residues: 134 loop : -1.24 (0.36), residues: 272 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 0.003 0.000 PHE A 139 TRP 0.008 0.001 TRP B 67 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.09 ( 6353) covalent geometry : angle 0.45456 / 0.24 ( 8773) hydrogen bonds : bond 0.03440 / 2.25 ( 294) hydrogen bonds : angle 3.18969 / 2.11 ( 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 44 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.205 Fit side-chains REVERT: A 106 GLU cc_start: 0.6070 (tm-30) cc_final: 0.5855 (tp30) REVERT: B 229 ARG cc_start: 0.7455 (mtm110) cc_final: 0.6934 (mtt180) REVERT: B 339 LEU cc_start: 0.7717 (pt) cc_final: 0.7202 (tp) outliers start: 4 outliers final: 4 residues processed: 43 average time/residue: 0.1278 time to fit residues: 6.8101 Evaluate side-chains 41 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.0000 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS B 10 ASN B 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143073 restraints weight = 7004.259| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.65 r_work: 0.3509 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6353 Z= 0.100 Angle : 0.467 5.947 8773 Z= 0.242 Chirality : 0.035 0.139 973 Planarity : 0.004 0.031 1011 Dihedral : 19.746 59.151 1187 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.15 % Allowed : 12.60 % 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: 1.19 (0.33), residues: 679 helix: 2.31 (0.32), residues: 277 sheet: 1.23 (0.44), residues: 138 loop : -1.18 (0.37), residues: 264 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 0.001 PHE A 139 TRP 0.004 0.001 TRP B 171 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 6353) covalent geometry : angle 0.46699 / 0.24 ( 8773) hydrogen bonds : bond 0.03706 / 2.43 ( 294) hydrogen bonds : angle 3.16903 / 2.10 ( 773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1612.56 seconds wall clock time: 28 minutes 10.53 seconds (1690.53 seconds total)