Starting phenix.real_space_refine on Sun Apr 5 12:17:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckv_16703/04_2026/8ckv_16703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckv_16703/04_2026/8ckv_16703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ckv_16703/04_2026/8ckv_16703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckv_16703/04_2026/8ckv_16703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ckv_16703/04_2026/8ckv_16703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckv_16703/04_2026/8ckv_16703.map" } resolution = 2.89 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= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 732 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6252 2.51 5 N 1716 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9900 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.46, per 1000 atoms: 0.15 Number of scatterers: 9900 At special positions: 0 Unit cell: (110.67, 112.53, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1860 8.00 N 1716 7.00 C 6252 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: 0.80 Conformation dependent library (CDL) restraints added in 506.5 milliseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 72.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.849A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 119 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.849A pdb=" N ALA F 174 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'F' and resid 2 through 4 618 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3300 1.34 - 1.46: 1250 1.46 - 1.58: 5428 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10110 Sorted by residual: bond pdb=" CB PRO E 1 " pdb=" CG PRO E 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.38e+00 bond pdb=" CB PRO B 1 " pdb=" CG PRO B 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.38e+00 bond pdb=" CB PRO F 1 " pdb=" CG PRO F 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.37e+00 bond pdb=" CB PRO C 1 " pdb=" CG PRO C 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.37e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.37e+00 ... (remaining 10105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 11922 1.11 - 2.22: 1490 2.22 - 3.32: 244 3.32 - 4.43: 66 4.43 - 5.54: 12 Bond angle restraints: 13734 Sorted by residual: angle pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.66e+00 angle pdb=" C GLU F 175 " pdb=" N GLN F 176 " pdb=" CA GLN F 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.66e+00 angle pdb=" C GLU A 175 " pdb=" N GLN A 176 " pdb=" CA GLN A 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.63e+00 angle pdb=" C GLU D 175 " pdb=" N GLN D 176 " pdb=" CA GLN D 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.63e+00 angle pdb=" C GLU B 175 " pdb=" N GLN B 176 " pdb=" CA GLN B 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.63e+00 ... (remaining 13729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 5610 15.32 - 30.63: 432 30.63 - 45.95: 132 45.95 - 61.26: 12 61.26 - 76.57: 6 Dihedral angle restraints: 6192 sinusoidal: 2520 harmonic: 3672 Sorted by residual: dihedral pdb=" CA ASN D 121 " pdb=" C ASN D 121 " pdb=" N PRO D 122 " pdb=" CA PRO D 122 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " pdb=" CA PRO A 122 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN E 121 " pdb=" C ASN E 121 " pdb=" N PRO E 122 " pdb=" CA PRO E 122 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 735 0.032 - 0.064: 535 0.064 - 0.095: 178 0.095 - 0.127: 76 0.127 - 0.159: 30 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA PHE F 32 " pdb=" N PHE F 32 " pdb=" C PHE F 32 " pdb=" CB PHE F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE C 32 " pdb=" N PHE C 32 " pdb=" C PHE C 32 " pdb=" CB PHE C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE D 32 " pdb=" N PHE D 32 " pdb=" C PHE D 32 " pdb=" CB PHE D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 1551 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 173 " -0.207 9.50e-02 1.11e+02 9.29e-02 5.33e+00 pdb=" NE ARG B 173 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 173 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 173 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 173 " 0.207 9.50e-02 1.11e+02 9.29e-02 5.33e+00 pdb=" NE ARG E 173 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 173 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 173 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 173 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 173 " -0.206 9.50e-02 1.11e+02 9.24e-02 5.28e+00 pdb=" NE ARG C 173 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 173 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 173 " -0.006 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 12 1.90 - 2.65: 54 2.65 - 3.40: 14330 3.40 - 4.15: 24026 4.15 - 4.90: 44676 Nonbonded interactions: 83098 Sorted by model distance: nonbonded pdb=" NH2 ARG B 18 " pdb=" NH1 ARG C 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG E 18 " pdb=" NH1 ARG F 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG A 18 " pdb=" NH1 ARG B 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG D 18 " pdb=" NH1 ARG E 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG C 18 " pdb=" NH1 ARG D 18 " model vdw 1.153 3.200 ... (remaining 83093 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.080 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.004 0.077 10110 Z= 0.219 Angle : 0.823 5.537 13734 Z= 0.498 Chirality : 0.050 0.159 1554 Planarity : 0.011 0.093 1776 Dihedral : 12.341 76.573 3804 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.51 (0.20), residues: 1248 helix: -0.38 (0.15), residues: 840 sheet: -0.62 (0.39), residues: 54 loop : 0.31 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG C 97 TYR 0.018 0.005 TYR D 145 PHE 0.011 0.003 PHE E 40 TRP 0.014 0.004 TRP F 117 HIS 0.012 0.005 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00449 (10110) covalent geometry : angle 0.82293 (13734) hydrogen bonds : bond 0.10966 ( 618) hydrogen bonds : angle 6.41310 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.401 Fit side-chains REVERT: A 167 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7780 (mtp-110) REVERT: A 215 MET cc_start: 0.7895 (mtp) cc_final: 0.7523 (mtp) REVERT: B 33 SER cc_start: 0.8336 (t) cc_final: 0.8081 (m) REVERT: B 68 MET cc_start: 0.8460 (mtp) cc_final: 0.8157 (mtp) REVERT: B 163 ASP cc_start: 0.7498 (m-30) cc_final: 0.7276 (m-30) REVERT: B 170 LYS cc_start: 0.8290 (tttm) cc_final: 0.8067 (tttp) REVERT: C 68 MET cc_start: 0.8434 (mtp) cc_final: 0.8205 (mtm) REVERT: D 167 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7781 (mtp-110) REVERT: D 215 MET cc_start: 0.7897 (mtp) cc_final: 0.7524 (mtp) REVERT: E 33 SER cc_start: 0.8339 (t) cc_final: 0.8083 (m) REVERT: E 68 MET cc_start: 0.8459 (mtp) cc_final: 0.8157 (mtp) REVERT: E 163 ASP cc_start: 0.7495 (m-30) cc_final: 0.7275 (m-30) REVERT: E 170 LYS cc_start: 0.8290 (tttm) cc_final: 0.8067 (tttp) REVERT: F 68 MET cc_start: 0.8433 (mtp) cc_final: 0.8205 (mtm) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.6416 time to fit residues: 154.3116 Evaluate side-chains 180 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0370 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.167719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.130947 restraints weight = 9480.392| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.73 r_work: 0.3163 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10110 Z= 0.155 Angle : 0.555 5.478 13734 Z= 0.284 Chirality : 0.042 0.127 1554 Planarity : 0.006 0.066 1776 Dihedral : 5.100 29.407 1344 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.87 % Allowed : 7.30 % Favored : 90.82 % 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: 1.34 (0.22), residues: 1248 helix: 1.33 (0.17), residues: 858 sheet: -0.17 (0.51), residues: 54 loop : 0.16 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 18 TYR 0.012 0.002 TYR D 169 PHE 0.011 0.002 PHE E 32 TRP 0.012 0.001 TRP C 117 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00382 (10110) covalent geometry : angle 0.55460 (13734) hydrogen bonds : bond 0.03853 ( 618) hydrogen bonds : angle 4.17784 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.364 Fit side-chains REVERT: A 144 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7773 (mtp) REVERT: A 154 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7387 (mtt-85) REVERT: A 193 ASN cc_start: 0.7932 (m110) cc_final: 0.7715 (m-40) REVERT: C 55 MET cc_start: 0.8809 (mtp) cc_final: 0.8554 (mtp) REVERT: C 159 GLU cc_start: 0.7225 (tt0) cc_final: 0.6988 (tt0) REVERT: C 180 GLU cc_start: 0.7260 (tt0) cc_final: 0.6642 (tp30) REVERT: D 144 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7761 (mtp) REVERT: D 154 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7383 (mtt-85) REVERT: D 193 ASN cc_start: 0.7929 (m110) cc_final: 0.7710 (m-40) REVERT: F 55 MET cc_start: 0.8807 (mtp) cc_final: 0.8552 (mtp) REVERT: F 159 GLU cc_start: 0.7227 (tt0) cc_final: 0.6993 (tt0) REVERT: F 180 GLU cc_start: 0.7273 (tt0) cc_final: 0.6645 (tp30) outliers start: 20 outliers final: 4 residues processed: 150 average time/residue: 0.6402 time to fit residues: 102.3977 Evaluate side-chains 138 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 0.0670 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.162321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.123871 restraints weight = 9630.190| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.80 r_work: 0.3078 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10110 Z= 0.240 Angle : 0.603 5.924 13734 Z= 0.304 Chirality : 0.046 0.147 1554 Planarity : 0.006 0.037 1776 Dihedral : 5.336 29.347 1344 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.87 % Allowed : 8.05 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.22), residues: 1248 helix: 1.00 (0.17), residues: 858 sheet: 0.24 (0.46), residues: 54 loop : 0.18 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 154 TYR 0.015 0.002 TYR C 169 PHE 0.014 0.003 PHE B 32 TRP 0.007 0.002 TRP A 184 HIS 0.006 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00616 (10110) covalent geometry : angle 0.60345 (13734) hydrogen bonds : bond 0.04541 ( 618) hydrogen bonds : angle 4.24356 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.463 Fit side-chains REVERT: A 71 GLU cc_start: 0.8337 (pt0) cc_final: 0.8044 (mt-10) REVERT: A 144 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7832 (mtp) REVERT: A 159 GLU cc_start: 0.7310 (tt0) cc_final: 0.7076 (tt0) REVERT: A 193 ASN cc_start: 0.8086 (m110) cc_final: 0.7873 (m-40) REVERT: C 71 GLU cc_start: 0.8320 (pt0) cc_final: 0.8039 (mt-10) REVERT: D 71 GLU cc_start: 0.8365 (pt0) cc_final: 0.8063 (mt-10) REVERT: D 144 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7827 (mtp) REVERT: D 159 GLU cc_start: 0.7309 (tt0) cc_final: 0.7072 (tt0) REVERT: D 193 ASN cc_start: 0.8090 (m110) cc_final: 0.7878 (m-40) REVERT: F 71 GLU cc_start: 0.8318 (pt0) cc_final: 0.8047 (mt-10) outliers start: 20 outliers final: 8 residues processed: 172 average time/residue: 0.6455 time to fit residues: 118.3875 Evaluate side-chains 158 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.166087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.128134 restraints weight = 9627.171| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.78 r_work: 0.3134 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10110 Z= 0.135 Angle : 0.495 5.234 13734 Z= 0.248 Chirality : 0.041 0.129 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.735 28.064 1344 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.62 % Allowed : 9.74 % Favored : 87.64 % 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: 1.42 (0.23), residues: 1248 helix: 1.37 (0.18), residues: 858 sheet: 0.14 (0.49), residues: 54 loop : 0.18 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.012 0.001 TYR F 169 PHE 0.012 0.002 PHE B 32 TRP 0.006 0.001 TRP D 184 HIS 0.003 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00337 (10110) covalent geometry : angle 0.49534 (13734) hydrogen bonds : bond 0.03591 ( 618) hydrogen bonds : angle 3.86895 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.271 Fit side-chains REVERT: A 144 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7646 (mtp) REVERT: A 159 GLU cc_start: 0.7244 (tt0) cc_final: 0.6980 (tt0) REVERT: A 193 ASN cc_start: 0.8075 (m110) cc_final: 0.7852 (m-40) REVERT: B 144 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7887 (mtp) REVERT: B 159 GLU cc_start: 0.7411 (tt0) cc_final: 0.7150 (tt0) REVERT: C 71 GLU cc_start: 0.8214 (pt0) cc_final: 0.7972 (mt-10) REVERT: C 144 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7931 (mtp) REVERT: C 159 GLU cc_start: 0.6948 (tt0) cc_final: 0.6601 (tt0) REVERT: D 144 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7639 (mtp) REVERT: D 159 GLU cc_start: 0.7239 (tt0) cc_final: 0.6969 (tt0) REVERT: D 193 ASN cc_start: 0.8078 (m110) cc_final: 0.7856 (m-40) REVERT: E 144 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7896 (mtp) REVERT: E 159 GLU cc_start: 0.7409 (tt0) cc_final: 0.7149 (tt0) REVERT: F 71 GLU cc_start: 0.8224 (pt0) cc_final: 0.7983 (mt-10) REVERT: F 144 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7936 (mtp) REVERT: F 159 GLU cc_start: 0.6944 (tt0) cc_final: 0.6586 (tt0) outliers start: 28 outliers final: 6 residues processed: 148 average time/residue: 0.6265 time to fit residues: 98.8238 Evaluate side-chains 142 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.167795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130146 restraints weight = 9492.671| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.77 r_work: 0.3157 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10110 Z= 0.119 Angle : 0.470 5.048 13734 Z= 0.234 Chirality : 0.040 0.123 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.418 26.170 1344 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.87 % Allowed : 10.49 % Favored : 87.64 % 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: 1.67 (0.23), residues: 1248 helix: 1.56 (0.18), residues: 858 sheet: 0.27 (0.55), residues: 54 loop : 0.25 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 154 TYR 0.011 0.001 TYR C 169 PHE 0.011 0.002 PHE E 32 TRP 0.005 0.001 TRP A 184 HIS 0.003 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00292 (10110) covalent geometry : angle 0.46999 (13734) hydrogen bonds : bond 0.03350 ( 618) hydrogen bonds : angle 3.67678 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.365 Fit side-chains REVERT: A 159 GLU cc_start: 0.7198 (tt0) cc_final: 0.6962 (tt0) REVERT: A 193 ASN cc_start: 0.8108 (m110) cc_final: 0.7885 (m-40) REVERT: B 159 GLU cc_start: 0.7314 (tt0) cc_final: 0.7082 (tt0) REVERT: C 159 GLU cc_start: 0.6877 (tt0) cc_final: 0.6596 (tt0) REVERT: D 159 GLU cc_start: 0.7183 (tt0) cc_final: 0.6950 (tt0) REVERT: D 193 ASN cc_start: 0.8117 (m110) cc_final: 0.7893 (m-40) REVERT: E 159 GLU cc_start: 0.7319 (tt0) cc_final: 0.7088 (tt0) REVERT: F 159 GLU cc_start: 0.6875 (tt0) cc_final: 0.6603 (tt0) outliers start: 20 outliers final: 8 residues processed: 142 average time/residue: 0.6392 time to fit residues: 96.8265 Evaluate side-chains 132 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.164745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126259 restraints weight = 9613.542| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.79 r_work: 0.3102 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10110 Z= 0.173 Angle : 0.518 5.195 13734 Z= 0.258 Chirality : 0.042 0.131 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.690 27.004 1344 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.97 % Allowed : 10.96 % Favored : 87.08 % 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: 1.35 (0.23), residues: 1248 helix: 1.27 (0.18), residues: 858 sheet: 0.32 (0.50), residues: 54 loop : 0.27 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.014 0.001 TYR C 169 PHE 0.011 0.002 PHE B 32 TRP 0.006 0.001 TRP E 184 HIS 0.004 0.002 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00440 (10110) covalent geometry : angle 0.51790 (13734) hydrogen bonds : bond 0.03898 ( 618) hydrogen bonds : angle 3.88134 ( 1818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.366 Fit side-chains REVERT: A 71 GLU cc_start: 0.8279 (pt0) cc_final: 0.8007 (mt-10) REVERT: A 159 GLU cc_start: 0.7270 (tt0) cc_final: 0.7024 (tt0) REVERT: A 193 ASN cc_start: 0.8112 (m110) cc_final: 0.7888 (m-40) REVERT: B 159 GLU cc_start: 0.7418 (tt0) cc_final: 0.7170 (tt0) REVERT: C 159 GLU cc_start: 0.7073 (tt0) cc_final: 0.6611 (tt0) REVERT: D 71 GLU cc_start: 0.8296 (pt0) cc_final: 0.8014 (mt-10) REVERT: D 159 GLU cc_start: 0.7264 (tt0) cc_final: 0.7020 (tt0) REVERT: D 193 ASN cc_start: 0.8116 (m110) cc_final: 0.7888 (m-40) REVERT: E 159 GLU cc_start: 0.7407 (tt0) cc_final: 0.7161 (tt0) REVERT: F 159 GLU cc_start: 0.7059 (tt0) cc_final: 0.6598 (tt0) outliers start: 21 outliers final: 15 residues processed: 153 average time/residue: 0.6180 time to fit residues: 101.0336 Evaluate side-chains 147 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 103 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.166906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128862 restraints weight = 9487.843| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.78 r_work: 0.3134 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10110 Z= 0.129 Angle : 0.481 4.997 13734 Z= 0.238 Chirality : 0.040 0.125 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.437 25.890 1344 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.40 % Allowed : 11.52 % Favored : 87.08 % 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: 1.55 (0.23), residues: 1248 helix: 1.44 (0.18), residues: 858 sheet: 0.30 (0.52), residues: 54 loop : 0.29 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 154 TYR 0.012 0.001 TYR C 169 PHE 0.012 0.002 PHE B 32 TRP 0.005 0.001 TRP A 184 HIS 0.003 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00322 (10110) covalent geometry : angle 0.48131 (13734) hydrogen bonds : bond 0.03487 ( 618) hydrogen bonds : angle 3.75289 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.287 Fit side-chains REVERT: A 71 GLU cc_start: 0.8268 (pt0) cc_final: 0.8016 (mt-10) REVERT: A 159 GLU cc_start: 0.7239 (tt0) cc_final: 0.7022 (tt0) REVERT: A 193 ASN cc_start: 0.8085 (m110) cc_final: 0.7857 (m-40) REVERT: B 159 GLU cc_start: 0.7355 (tt0) cc_final: 0.7105 (tt0) REVERT: C 159 GLU cc_start: 0.6930 (tt0) cc_final: 0.6574 (tt0) REVERT: D 71 GLU cc_start: 0.8266 (pt0) cc_final: 0.7998 (mt-10) REVERT: D 159 GLU cc_start: 0.7227 (tt0) cc_final: 0.7014 (tt0) REVERT: D 193 ASN cc_start: 0.8082 (m110) cc_final: 0.7851 (m-40) REVERT: E 159 GLU cc_start: 0.7359 (tt0) cc_final: 0.7110 (tt0) REVERT: F 159 GLU cc_start: 0.6921 (tt0) cc_final: 0.6561 (tt0) outliers start: 15 outliers final: 7 residues processed: 144 average time/residue: 0.6275 time to fit residues: 96.3095 Evaluate side-chains 135 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.0370 chunk 57 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.167863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.129788 restraints weight = 9473.049| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.78 r_work: 0.3142 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10110 Z= 0.121 Angle : 0.476 5.573 13734 Z= 0.233 Chirality : 0.040 0.122 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.305 25.262 1344 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.06 % Allowed : 10.96 % Favored : 86.99 % 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: 1.63 (0.23), residues: 1248 helix: 1.50 (0.18), residues: 858 sheet: 0.33 (0.54), residues: 54 loop : 0.32 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 154 TYR 0.011 0.001 TYR F 169 PHE 0.011 0.002 PHE E 32 TRP 0.005 0.001 TRP A 184 HIS 0.003 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00298 (10110) covalent geometry : angle 0.47641 (13734) hydrogen bonds : bond 0.03420 ( 618) hydrogen bonds : angle 3.70451 ( 1818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.343 Fit side-chains REVERT: A 71 GLU cc_start: 0.8229 (pt0) cc_final: 0.7987 (mt-10) REVERT: A 159 GLU cc_start: 0.7189 (tt0) cc_final: 0.6966 (tt0) REVERT: A 193 ASN cc_start: 0.8022 (m110) cc_final: 0.7817 (m-40) REVERT: B 159 GLU cc_start: 0.7337 (tt0) cc_final: 0.7072 (tt0) REVERT: B 192 GLN cc_start: 0.7289 (mt0) cc_final: 0.6928 (mt0) REVERT: C 159 GLU cc_start: 0.6766 (tt0) cc_final: 0.6496 (tt0) REVERT: D 71 GLU cc_start: 0.8237 (pt0) cc_final: 0.7982 (mt-10) REVERT: D 159 GLU cc_start: 0.7180 (tt0) cc_final: 0.6961 (tt0) REVERT: D 193 ASN cc_start: 0.8020 (m110) cc_final: 0.7810 (m-40) REVERT: E 159 GLU cc_start: 0.7331 (tt0) cc_final: 0.7067 (tt0) REVERT: E 192 GLN cc_start: 0.7285 (mt0) cc_final: 0.6919 (mt0) REVERT: F 159 GLU cc_start: 0.6758 (tt0) cc_final: 0.6485 (tt0) outliers start: 22 outliers final: 10 residues processed: 146 average time/residue: 0.6497 time to fit residues: 100.9499 Evaluate side-chains 136 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 216 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 110 optimal weight: 0.3980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.168280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.131164 restraints weight = 9517.673| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.75 r_work: 0.3154 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10110 Z= 0.114 Angle : 0.474 5.938 13734 Z= 0.231 Chirality : 0.040 0.122 1554 Planarity : 0.004 0.037 1776 Dihedral : 4.214 24.630 1344 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.59 % Allowed : 11.70 % Favored : 86.70 % 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: 1.71 (0.23), residues: 1248 helix: 1.56 (0.18), residues: 858 sheet: 0.29 (0.55), residues: 54 loop : 0.37 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.011 0.001 TYR B 169 PHE 0.011 0.002 PHE E 32 TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00279 (10110) covalent geometry : angle 0.47405 (13734) hydrogen bonds : bond 0.03384 ( 618) hydrogen bonds : angle 3.67497 ( 1818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.394 Fit side-chains REVERT: A 193 ASN cc_start: 0.8036 (m110) cc_final: 0.7823 (m-40) REVERT: B 159 GLU cc_start: 0.7332 (tt0) cc_final: 0.7076 (tt0) REVERT: B 192 GLN cc_start: 0.7296 (mt0) cc_final: 0.6954 (mt0) REVERT: C 159 GLU cc_start: 0.6732 (tt0) cc_final: 0.6492 (tt0) REVERT: D 159 GLU cc_start: 0.7153 (tt0) cc_final: 0.6941 (tt0) REVERT: D 193 ASN cc_start: 0.8030 (m110) cc_final: 0.7799 (m-40) REVERT: E 159 GLU cc_start: 0.7333 (tt0) cc_final: 0.7059 (tt0) REVERT: E 192 GLN cc_start: 0.7310 (mt0) cc_final: 0.6967 (mt0) REVERT: F 159 GLU cc_start: 0.6714 (tt0) cc_final: 0.6477 (tt0) outliers start: 17 outliers final: 7 residues processed: 139 average time/residue: 0.6260 time to fit residues: 93.0452 Evaluate side-chains 135 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.164738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.126458 restraints weight = 9596.370| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.79 r_work: 0.3096 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10110 Z= 0.191 Angle : 0.550 8.243 13734 Z= 0.269 Chirality : 0.043 0.132 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.665 26.087 1344 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.78 % Allowed : 11.33 % Favored : 86.89 % 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: 1.23 (0.23), residues: 1248 helix: 1.15 (0.18), residues: 858 sheet: 0.17 (0.48), residues: 54 loop : 0.32 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 173 TYR 0.015 0.002 TYR C 169 PHE 0.010 0.002 PHE E 32 TRP 0.006 0.001 TRP F 23 HIS 0.005 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00487 (10110) covalent geometry : angle 0.55040 (13734) hydrogen bonds : bond 0.04119 ( 618) hydrogen bonds : angle 3.93798 ( 1818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.378 Fit side-chains REVERT: A 71 GLU cc_start: 0.8343 (pt0) cc_final: 0.8068 (mt-10) REVERT: A 193 ASN cc_start: 0.8036 (m110) cc_final: 0.7798 (m-40) REVERT: B 154 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.7114 (mtm-85) REVERT: B 159 GLU cc_start: 0.7337 (tt0) cc_final: 0.7055 (tt0) REVERT: C 159 GLU cc_start: 0.7020 (tt0) cc_final: 0.6618 (tt0) REVERT: D 71 GLU cc_start: 0.8355 (pt0) cc_final: 0.8075 (mt-10) REVERT: D 159 GLU cc_start: 0.7253 (tt0) cc_final: 0.7005 (tt0) REVERT: D 193 ASN cc_start: 0.8025 (m110) cc_final: 0.7791 (m-40) REVERT: E 154 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.7126 (mtm-85) REVERT: E 159 GLU cc_start: 0.7331 (tt0) cc_final: 0.7053 (tt0) REVERT: F 159 GLU cc_start: 0.7006 (tt0) cc_final: 0.6603 (tt0) outliers start: 19 outliers final: 12 residues processed: 149 average time/residue: 0.6073 time to fit residues: 96.8368 Evaluate side-chains 146 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 108 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.167755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.129773 restraints weight = 9605.888| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.78 r_work: 0.3148 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10110 Z= 0.123 Angle : 0.493 7.420 13734 Z= 0.240 Chirality : 0.040 0.124 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.364 25.321 1344 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.31 % Allowed : 12.27 % Favored : 86.42 % 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: 1.49 (0.23), residues: 1248 helix: 1.36 (0.18), residues: 858 sheet: 0.20 (0.53), residues: 54 loop : 0.38 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 154 TYR 0.012 0.001 TYR B 169 PHE 0.012 0.002 PHE E 32 TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00301 (10110) covalent geometry : angle 0.49272 (13734) hydrogen bonds : bond 0.03569 ( 618) hydrogen bonds : angle 3.78284 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.94 seconds wall clock time: 65 minutes 53.19 seconds (3953.19 seconds total)