Starting phenix.real_space_refine on Tue Mar 3 14:42:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8j_15231/03_2026/8a8j_15231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8j_15231/03_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_15231/03_2026/8a8j_15231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8j_15231/03_2026/8a8j_15231.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8j_15231/03_2026/8a8j_15231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8j_15231/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 1.96, 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: 0.67 Conformation dependent library (CDL) restraints added in 220.8 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: 0.56 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: 1.03 Time building geometry restraints manager: 0.78 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=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O2B ANP A 901 " ideal model delta sigma weight residual 120.08 109.17 10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O2B ANP B 901 " ideal model delta sigma weight residual 120.08 109.51 10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " pdb=" O2G ANP A 901 " ideal model delta sigma weight residual 101.05 110.86 -9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 8768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 3096 17.62 - 35.24: 413 35.24 - 52.86: 204 52.86 - 70.48: 37 70.48 - 88.10: 14 Dihedral angle restraints: 3764 sinusoidal: 1830 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 3761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 868 0.056 - 0.112: 90 0.112 - 0.169: 13 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: 2.880 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.580 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 6353 Z= 0.244 Angle : 0.706 14.342 8773 Z= 0.316 Chirality : 0.039 0.281 973 Planarity : 0.005 0.058 1011 Dihedral : 19.597 88.099 2526 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 covalent geometry : bond 0.00518 ( 6353) covalent geometry : angle 0.70638 ( 8773) hydrogen bonds : bond 0.22158 ( 294) hydrogen bonds : angle 6.66961 ( 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 : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1888 time to fit residues: 11.5502 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 : 0.199 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135158 restraints weight = 13490.839| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.54 r_work: 0.3348 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 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 = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6353 Z= 0.130 Angle : 0.544 6.019 8773 Z= 0.280 Chirality : 0.037 0.131 973 Planarity : 0.005 0.033 1011 Dihedral : 20.246 89.425 1243 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: 0.46 (0.33), residues: 679 helix: 1.72 (0.32), residues: 277 sheet: 0.91 (0.46), residues: 128 loop : -1.55 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 2 TYR 0.008 0.001 TYR B 150 PHE 0.006 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 covalent geometry : bond 0.00291 ( 6353) covalent geometry : angle 0.54418 ( 8773) hydrogen bonds : bond 0.05273 ( 294) hydrogen bonds : angle 3.89457 ( 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 50 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.213 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1641 time to fit residues: 9.6668 Evaluate side-chains 49 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.0020 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.169746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137623 restraints weight = 9166.562| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.05 r_work: 0.3411 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1124 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 : 0.495 5.529 8773 Z= 0.255 Chirality : 0.036 0.127 973 Planarity : 0.004 0.033 1011 Dihedral : 19.815 86.699 1243 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.95 % Allowed : 6.87 % Favored : 92.18 % 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: 0.69 (0.33), residues: 679 helix: 1.92 (0.32), residues: 277 sheet: 1.12 (0.46), residues: 128 loop : -1.49 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 229 TYR 0.008 0.001 TYR B 150 PHE 0.004 0.001 PHE A 139 TRP 0.004 0.001 TRP B 171 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6353) covalent geometry : angle 0.49523 ( 8773) hydrogen bonds : bond 0.04468 ( 294) hydrogen bonds : angle 3.56615 ( 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 : 0.170 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.1601 time to fit residues: 9.3057 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 : 0.143 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.0270 chunk 54 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.169298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134099 restraints weight = 14676.403| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.67 r_work: 0.3354 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6353 Z= 0.128 Angle : 0.516 5.680 8773 Z= 0.264 Chirality : 0.037 0.145 973 Planarity : 0.004 0.034 1011 Dihedral : 19.660 88.360 1243 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.15 % Allowed : 9.54 % Favored : 89.31 % 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 (0.32), residues: 679 helix: 1.89 (0.32), residues: 277 sheet: 1.35 (0.46), residues: 124 loop : -1.59 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 229 TYR 0.008 0.001 TYR B 150 PHE 0.005 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 covalent geometry : bond 0.00295 ( 6353) covalent geometry : angle 0.51649 ( 8773) hydrogen bonds : bond 0.04728 ( 294) hydrogen bonds : angle 3.48132 ( 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 49 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.242 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.1556 time to fit residues: 8.8864 Evaluate side-chains 45 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 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=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: 5.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.0030 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.0040 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 23 optimal weight: 0.8980 overall best weight: 0.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137993 restraints weight = 13431.275| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.54 r_work: 0.3422 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6353 Z= 0.101 Angle : 0.460 5.660 8773 Z= 0.238 Chirality : 0.035 0.140 973 Planarity : 0.004 0.033 1011 Dihedral : 19.494 84.758 1243 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.76 % Allowed : 10.69 % 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: 0.93 (0.33), residues: 679 helix: 2.10 (0.32), residues: 279 sheet: 1.06 (0.45), residues: 138 loop : -1.34 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 223 TYR 0.008 0.001 TYR B 150 PHE 0.003 0.000 PHE A 139 TRP 0.005 0.001 TRP B 171 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6353) covalent geometry : angle 0.46000 ( 8773) hydrogen bonds : bond 0.03742 ( 294) hydrogen bonds : angle 3.27338 ( 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 48 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.185 Fit side-chains REVERT: B 229 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6860 (mtt180) REVERT: B 339 LEU cc_start: 0.7727 (pt) cc_final: 0.7200 (tp) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1569 time to fit residues: 8.9568 Evaluate side-chains 43 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.171266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138106 restraints weight = 10725.510| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.21 r_work: 0.3402 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1389 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= 0.112 Angle : 0.480 5.260 8773 Z= 0.246 Chirality : 0.035 0.136 973 Planarity : 0.004 0.031 1011 Dihedral : 19.496 85.220 1243 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.95 % Allowed : 10.88 % Favored : 88.17 % 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: 2.12 (0.32), residues: 277 sheet: 1.03 (0.44), residues: 138 loop : -1.33 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 223 TYR 0.007 0.001 TYR B 150 PHE 0.006 0.001 PHE A 139 TRP 0.004 0.001 TRP B 105 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6353) covalent geometry : angle 0.47954 ( 8773) hydrogen bonds : bond 0.04095 ( 294) hydrogen bonds : angle 3.27424 ( 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 46 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.269 Fit side-chains REVERT: B 339 LEU cc_start: 0.7726 (pt) cc_final: 0.7205 (tp) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.1464 time to fit residues: 8.1139 Evaluate side-chains 43 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3916 r_free = 0.3916 target = 0.169052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134280 restraints weight = 13406.567| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.51 r_work: 0.3344 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6353 Z= 0.139 Angle : 0.525 5.560 8773 Z= 0.267 Chirality : 0.037 0.135 973 Planarity : 0.004 0.033 1011 Dihedral : 19.585 87.884 1243 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: 0.83 (0.33), residues: 679 helix: 2.01 (0.32), residues: 277 sheet: 1.16 (0.45), residues: 134 loop : -1.42 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 229 TYR 0.009 0.001 TYR B 150 PHE 0.007 0.001 PHE A 139 TRP 0.004 0.001 TRP A 105 HIS 0.006 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6353) covalent geometry : angle 0.52499 ( 8773) hydrogen bonds : bond 0.04788 ( 294) hydrogen bonds : angle 3.35982 ( 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: 4 poor density : 46 time to evaluate : 0.217 Fit side-chains REVERT: A 226 GLU cc_start: 0.8168 (tt0) cc_final: 0.7959 (tm-30) REVERT: B 122 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8411 (pp) REVERT: B 229 ARG cc_start: 0.7412 (mtm110) cc_final: 0.6818 (mtt180) REVERT: B 339 LEU cc_start: 0.7749 (pt) cc_final: 0.7244 (tp) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.1494 time to fit residues: 8.8987 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 : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.171806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140063 restraints weight = 8924.283| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.94 r_work: 0.3437 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1474 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= 0.106 Angle : 0.474 6.343 8773 Z= 0.244 Chirality : 0.035 0.133 973 Planarity : 0.004 0.033 1011 Dihedral : 19.502 85.180 1243 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.34 % Allowed : 11.83 % 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: 1.00 (0.33), residues: 679 helix: 2.15 (0.32), residues: 277 sheet: 1.13 (0.45), residues: 138 loop : -1.29 (0.37), residues: 264 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 0.003 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6353) covalent geometry : angle 0.47391 ( 8773) hydrogen bonds : bond 0.03893 ( 294) hydrogen bonds : angle 3.23691 ( 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 53 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.184 Fit side-chains REVERT: A 106 GLU cc_start: 0.6207 (tm-30) cc_final: 0.5935 (tp30) REVERT: A 226 GLU cc_start: 0.8279 (tt0) cc_final: 0.7978 (tm-30) REVERT: A 339 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6857 (pp) REVERT: B 229 ARG cc_start: 0.7371 (mtm110) cc_final: 0.6774 (mtt180) REVERT: B 339 LEU cc_start: 0.7714 (pt) cc_final: 0.7233 (tp) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.1499 time to fit residues: 9.2056 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 : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 339 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: 0.7980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3926 r_free = 0.3926 target = 0.170002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138648 restraints weight = 10773.541| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.87 r_work: 0.3421 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6353 Z= 0.124 Angle : 0.512 6.420 8773 Z= 0.260 Chirality : 0.036 0.149 973 Planarity : 0.004 0.032 1011 Dihedral : 19.518 86.155 1243 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 0.93 (0.33), residues: 679 helix: 2.08 (0.32), residues: 277 sheet: 1.23 (0.45), residues: 134 loop : -1.36 (0.36), residues: 268 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 0.006 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 covalent geometry : bond 0.00288 ( 6353) covalent geometry : angle 0.51165 ( 8773) hydrogen bonds : bond 0.04376 ( 294) hydrogen bonds : angle 3.28089 ( 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 49 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.216 Fit side-chains REVERT: A 106 GLU cc_start: 0.6205 (tm-30) cc_final: 0.5976 (tp30) REVERT: A 226 GLU cc_start: 0.8279 (tt0) cc_final: 0.8026 (tm-30) REVERT: A 339 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7050 (pp) REVERT: B 229 ARG cc_start: 0.7440 (mtm110) cc_final: 0.6820 (mtt180) REVERT: B 339 LEU cc_start: 0.7790 (pt) cc_final: 0.7308 (tp) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1526 time to fit residues: 8.7728 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 339 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: 0.3980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3943 r_free = 0.3943 target = 0.171623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136330 restraints weight = 14704.075| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.67 r_work: 0.3370 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1518 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= 0.108 Angle : 0.485 6.358 8773 Z= 0.248 Chirality : 0.035 0.138 973 Planarity : 0.004 0.033 1011 Dihedral : 19.475 84.981 1243 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 1.04 (0.33), residues: 679 helix: 2.17 (0.32), residues: 277 sheet: 1.15 (0.45), residues: 138 loop : -1.26 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 covalent geometry : bond 0.00244 ( 6353) covalent geometry : angle 0.48474 ( 8773) hydrogen bonds : bond 0.03917 ( 294) hydrogen bonds : angle 3.20613 ( 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 48 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.268 Fit side-chains REVERT: A 226 GLU cc_start: 0.8185 (tt0) cc_final: 0.7936 (tm-30) REVERT: B 229 ARG cc_start: 0.7400 (mtm110) cc_final: 0.6819 (mtt180) REVERT: B 339 LEU cc_start: 0.7693 (pt) cc_final: 0.7215 (tp) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1537 time to fit residues: 8.7932 Evaluate side-chains 44 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=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: 0.9980 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3924 r_free = 0.3924 target = 0.169959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139737 restraints weight = 7018.167| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.66 r_work: 0.3440 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6353 Z= 0.125 Angle : 0.514 6.312 8773 Z= 0.259 Chirality : 0.036 0.158 973 Planarity : 0.004 0.033 1011 Dihedral : 19.498 85.866 1243 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.76 % Allowed : 12.40 % 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: 0.96 (0.33), residues: 679 helix: 2.08 (0.32), residues: 277 sheet: 1.24 (0.45), residues: 134 loop : -1.31 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 223 TYR 0.008 0.001 TYR B 150 PHE 0.005 0.001 PHE A 139 TRP 0.005 0.001 TRP A 105 HIS 0.005 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6353) covalent geometry : angle 0.51447 ( 8773) hydrogen bonds : bond 0.04373 ( 294) hydrogen bonds : angle 3.25531 ( 773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.94 seconds wall clock time: 30 minutes 19.31 seconds (1819.31 seconds total)