Starting phenix.real_space_refine on Tue Feb 3 16:31:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxw_43642/02_2026/8vxw_43642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxw_43642/02_2026/8vxw_43642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vxw_43642/02_2026/8vxw_43642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxw_43642/02_2026/8vxw_43642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vxw_43642/02_2026/8vxw_43642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxw_43642/02_2026/8vxw_43642.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.042 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: 3 Type Number sf(0) Gaussians C 2990 2.51 5 N 1015 2.21 5 O 1015 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5020 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1004 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'HIS:plan': 4, 'GLN:plan1': 11, 'ASN:plan1': 9, 'TRP:plan': 5, 'GLU:plan': 17, 'PHE:plan': 4, 'ASP:plan': 7, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 322 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1004 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'HIS:plan': 4, 'GLN:plan1': 11, 'ASN:plan1': 9, 'TRP:plan': 5, 'GLU:plan': 17, 'PHE:plan': 4, 'ASP:plan': 7, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 322 Chain: "C" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1004 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'HIS:plan': 4, 'GLN:plan1': 11, 'ASN:plan1': 9, 'TRP:plan': 5, 'GLU:plan': 17, 'PHE:plan': 4, 'ASP:plan': 7, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 322 Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1004 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'HIS:plan': 4, 'GLN:plan1': 11, 'ASN:plan1': 9, 'TRP:plan': 5, 'GLU:plan': 17, 'PHE:plan': 4, 'ASP:plan': 7, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 322 Chain: "E" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1004 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'HIS:plan': 4, 'GLN:plan1': 11, 'ASN:plan1': 9, 'TRP:plan': 5, 'GLU:plan': 17, 'PHE:plan': 4, 'ASP:plan': 7, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 322 Time building chain proxies: 1.57, per 1000 atoms: 0.31 Number of scatterers: 5020 At special positions: 0 Unit cell: (104.272, 101.528, 76.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1015 8.00 N 1015 7.00 C 2990 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: 0.49 Conformation dependent library (CDL) restraints added in 423.8 milliseconds 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.660A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.645A pdb=" N MET A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.775A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.732A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.600A pdb=" N MET B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.813A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.715A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.749A pdb=" N MET C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) 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 removed outlier: 3.557A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.740A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.749A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.772A pdb=" N MET D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) 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 removed outlier: 3.597A pdb=" N ALA D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) 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 removed outlier: 3.529A pdb=" N ASP D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.843A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.764A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.658A pdb=" N MET E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) 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 removed outlier: 3.539A pdb=" N ASP E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 194 removed outlier: 3.766A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 219 523 hydrogen bonds defined for protein. 1545 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: 0.75 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1015 1.29 - 1.36: 1000 1.36 - 1.43: 0 1.43 - 1.49: 1015 1.49 - 1.56: 1975 Bond restraints: 5005 Sorted by residual: bond pdb=" CA ASN A 195 " pdb=" CB ASN A 195 " ideal model delta sigma weight residual 1.526 1.545 -0.019 1.59e-02 3.96e+03 1.43e+00 bond pdb=" CA GLU C 76 " pdb=" CB GLU C 76 " ideal model delta sigma weight residual 1.528 1.546 -0.018 1.59e-02 3.96e+03 1.27e+00 bond pdb=" CA GLU B 76 " pdb=" CB GLU B 76 " ideal model delta sigma weight residual 1.528 1.547 -0.018 1.66e-02 3.63e+03 1.21e+00 bond pdb=" C THR C 48 " pdb=" N PRO C 49 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.36e-02 5.41e+03 8.85e-01 bond pdb=" CA THR C 48 " pdb=" C THR C 48 " ideal model delta sigma weight residual 1.525 1.537 -0.012 1.34e-02 5.57e+03 8.58e-01 ... (remaining 5000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 6724 1.36 - 2.72: 197 2.72 - 4.08: 24 4.08 - 5.44: 2 5.44 - 6.80: 3 Bond angle restraints: 6950 Sorted by residual: angle pdb=" N GLU C 76 " pdb=" CA GLU C 76 " pdb=" CB GLU C 76 " ideal model delta sigma weight residual 110.16 116.96 -6.80 1.48e+00 4.57e-01 2.11e+01 angle pdb=" N GLU B 76 " pdb=" CA GLU B 76 " pdb=" CB GLU B 76 " ideal model delta sigma weight residual 110.28 116.86 -6.58 1.55e+00 4.16e-01 1.80e+01 angle pdb=" N ASN A 195 " pdb=" CA ASN A 195 " pdb=" CB ASN A 195 " ideal model delta sigma weight residual 110.11 104.43 5.68 1.46e+00 4.69e-01 1.51e+01 angle pdb=" N TRP C 117 " pdb=" CA TRP C 117 " pdb=" CB TRP C 117 " ideal model delta sigma weight residual 110.12 113.96 -3.84 1.47e+00 4.63e-01 6.84e+00 angle pdb=" C MET C 144 " pdb=" CA MET C 144 " pdb=" CB MET C 144 " ideal model delta sigma weight residual 110.79 114.69 -3.90 1.66e+00 3.63e-01 5.51e+00 ... (remaining 6945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 2.83: 2412 2.83 - 5.65: 360 5.65 - 8.48: 91 8.48 - 11.31: 46 11.31 - 14.13: 11 Dihedral angle restraints: 2920 sinusoidal: 0 harmonic: 2920 Sorted by residual: dihedral pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CA ASN A 195 " pdb=" CB ASN A 195 " ideal model delta harmonic sigma weight residual 122.80 114.29 8.51 0 2.50e+00 1.60e-01 1.16e+01 dihedral pdb=" N GLU B 76 " pdb=" C GLU B 76 " pdb=" CA GLU B 76 " pdb=" CB GLU B 76 " ideal model delta harmonic sigma weight residual 122.80 129.90 -7.10 0 2.50e+00 1.60e-01 8.06e+00 dihedral pdb=" CA ALA A 47 " pdb=" C ALA A 47 " pdb=" N THR A 48 " pdb=" CA THR A 48 " ideal model delta harmonic sigma weight residual 180.00 165.87 14.13 0 5.00e+00 4.00e-02 7.99e+00 ... (remaining 2917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 751 0.051 - 0.102: 163 0.102 - 0.153: 39 0.153 - 0.204: 6 0.204 - 0.255: 1 Chirality restraints: 960 Sorted by residual: chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO A 196 " pdb=" N PRO A 196 " pdb=" C PRO A 196 " pdb=" CB PRO A 196 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA GLU E 28 " pdb=" N GLU E 28 " pdb=" C GLU E 28 " pdb=" CB GLU E 28 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 957 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 185 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C MET B 185 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 185 " -0.011 2.00e-02 2.50e+03 pdb=" N THR B 186 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 185 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C MET D 185 " -0.029 2.00e-02 2.50e+03 pdb=" O MET D 185 " 0.011 2.00e-02 2.50e+03 pdb=" N THR D 186 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 185 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C MET E 185 " -0.029 2.00e-02 2.50e+03 pdb=" O MET E 185 " 0.011 2.00e-02 2.50e+03 pdb=" N THR E 186 " 0.010 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.02: 3143 3.02 - 3.49: 5588 3.49 - 3.96: 6645 3.96 - 4.43: 6980 4.43 - 4.90: 10008 Nonbonded interactions: 32364 Sorted by model distance: nonbonded pdb=" O ILE A 124 " pdb=" N VAL A 126 " model vdw 2.545 3.120 nonbonded pdb=" O ILE C 124 " pdb=" N VAL C 126 " model vdw 2.573 3.120 nonbonded pdb=" O ILE D 124 " pdb=" N VAL D 126 " model vdw 2.623 3.120 nonbonded pdb=" O ILE B 124 " pdb=" N VAL B 126 " model vdw 2.624 3.120 nonbonded pdb=" O ARG E 97 " pdb=" CA GLU E 98 " model vdw 2.661 2.776 ... (remaining 32359 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 0.230 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.440 Find NCS groups from input model: 0.090 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: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.002 0.019 5005 Z= 0.153 Angle : 0.583 6.796 6950 Z= 0.392 Chirality : 0.046 0.255 960 Planarity : 0.003 0.018 1000 Dihedral : 3.979 14.133 1000 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.40 (0.26), residues: 985 helix: 1.83 (0.18), residues: 725 sheet: None (None), residues: 0 loop : 1.16 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 5005) covalent geometry : angle 0.58294 ( 6950) hydrogen bonds : bond 0.13180 ( 523) hydrogen bonds : angle 5.00404 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0220 time to fit residues: 2.4740 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.089475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076328 restraints weight = 23454.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077232 restraints weight = 17916.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078252 restraints weight = 13383.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078519 restraints weight = 10979.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078541 restraints weight = 9812.361| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5005 Z= 0.211 Angle : 0.465 5.106 6950 Z= 0.308 Chirality : 0.042 0.129 960 Planarity : 0.003 0.011 1000 Dihedral : 4.178 23.382 1000 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.91 (0.26), residues: 985 helix: 2.43 (0.19), residues: 745 sheet: None (None), residues: 0 loop : 0.35 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5005) covalent geometry : angle 0.46478 ( 6950) hydrogen bonds : bond 0.04937 ( 523) hydrogen bonds : angle 4.20040 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.187 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0235 time to fit residues: 2.6470 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 28 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.084041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069550 restraints weight = 23351.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.070493 restraints weight = 17634.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.071154 restraints weight = 14362.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.071604 restraints weight = 12385.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.071867 restraints weight = 11138.879| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 5005 Z= 0.272 Angle : 0.542 5.881 6950 Z= 0.367 Chirality : 0.045 0.135 960 Planarity : 0.003 0.016 1000 Dihedral : 4.734 22.380 1000 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.07 (0.26), residues: 985 helix: 1.91 (0.19), residues: 727 sheet: None (None), residues: 0 loop : -0.09 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 5005) covalent geometry : angle 0.54166 ( 6950) hydrogen bonds : bond 0.05638 ( 523) hydrogen bonds : angle 5.00828 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0219 time to fit residues: 2.4860 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 overall best weight: 7.3790 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.084389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069786 restraints weight = 23293.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070878 restraints weight = 16820.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.071554 restraints weight = 13280.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072156 restraints weight = 11220.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072484 restraints weight = 9865.587| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 5005 Z= 0.219 Angle : 0.451 4.511 6950 Z= 0.304 Chirality : 0.043 0.126 960 Planarity : 0.002 0.013 1000 Dihedral : 4.303 21.853 1000 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.18 (0.27), residues: 985 helix: 2.06 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 5005) covalent geometry : angle 0.45070 ( 6950) hydrogen bonds : bond 0.04629 ( 523) hydrogen bonds : angle 4.43272 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0241 time to fit residues: 2.7261 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 chunk 70 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 40.0000 chunk 68 optimal weight: 50.0000 chunk 30 optimal weight: 40.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.083335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068528 restraints weight = 23684.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.069627 restraints weight = 17140.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.070417 restraints weight = 13464.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070905 restraints weight = 11280.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.071339 restraints weight = 9982.139| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 5005 Z= 0.233 Angle : 0.477 5.005 6950 Z= 0.322 Chirality : 0.043 0.126 960 Planarity : 0.003 0.014 1000 Dihedral : 4.544 21.918 1000 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.89 (0.27), residues: 985 helix: 1.95 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.59 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 5005) covalent geometry : angle 0.47704 ( 6950) hydrogen bonds : bond 0.05118 ( 523) hydrogen bonds : angle 4.71537 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0224 time to fit residues: 2.5501 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 20.0000 chunk 71 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 13 optimal weight: 0.0470 chunk 3 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 overall best weight: 14.0094 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.079410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.064429 restraints weight = 24013.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.065458 restraints weight = 17558.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.066075 restraints weight = 13938.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.066654 restraints weight = 11927.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.066949 restraints weight = 10553.535| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.8066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.171 5005 Z= 0.404 Angle : 0.682 5.399 6950 Z= 0.470 Chirality : 0.048 0.142 960 Planarity : 0.004 0.018 1000 Dihedral : 5.608 24.489 1000 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.22 (0.25), residues: 985 helix: 0.47 (0.18), residues: 700 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 5005) covalent geometry : angle 0.68166 ( 6950) hydrogen bonds : bond 0.06958 ( 523) hydrogen bonds : angle 6.17588 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0201 time to fit residues: 2.2394 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 0.0870 chunk 97 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 17 optimal weight: 30.0000 overall best weight: 4.6264 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.085033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.070276 restraints weight = 23007.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.071420 restraints weight = 16501.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072255 restraints weight = 12852.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.072763 restraints weight = 10713.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073206 restraints weight = 9427.200| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 5005 Z= 0.144 Angle : 0.381 4.687 6950 Z= 0.251 Chirality : 0.041 0.123 960 Planarity : 0.002 0.012 1000 Dihedral : 4.109 21.367 1000 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.70 (0.28), residues: 985 helix: 1.93 (0.20), residues: 731 sheet: None (None), residues: 0 loop : -1.31 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5005) covalent geometry : angle 0.38150 ( 6950) hydrogen bonds : bond 0.03957 ( 523) hydrogen bonds : angle 4.07219 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0228 time to fit residues: 2.5702 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 1 optimal weight: 0.0370 chunk 89 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 37 optimal weight: 30.0000 overall best weight: 11.8070 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.080125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065365 restraints weight = 23889.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.066308 restraints weight = 17503.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.067058 restraints weight = 14015.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.067514 restraints weight = 11897.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067874 restraints weight = 10625.388| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.8095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 5005 Z= 0.344 Angle : 0.598 4.739 6950 Z= 0.413 Chirality : 0.046 0.135 960 Planarity : 0.004 0.017 1000 Dihedral : 5.137 23.715 1000 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.23 (0.26), residues: 985 helix: 0.87 (0.19), residues: 705 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 5005) covalent geometry : angle 0.59843 ( 6950) hydrogen bonds : bond 0.06288 ( 523) hydrogen bonds : angle 5.66926 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0228 time to fit residues: 2.5624 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 40.0000 chunk 50 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.084199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.069510 restraints weight = 23116.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.070551 restraints weight = 17008.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071129 restraints weight = 13508.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071752 restraints weight = 11595.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.072099 restraints weight = 10228.572| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.7935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 5005 Z= 0.192 Angle : 0.421 4.185 6950 Z= 0.283 Chirality : 0.042 0.124 960 Planarity : 0.002 0.014 1000 Dihedral : 4.312 21.463 1000 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.27 (0.28), residues: 985 helix: 1.67 (0.20), residues: 731 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5005) covalent geometry : angle 0.42067 ( 6950) hydrogen bonds : bond 0.04483 ( 523) hydrogen bonds : angle 4.44156 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0229 time to fit residues: 2.5757 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 31 optimal weight: 40.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.084484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.069808 restraints weight = 23250.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070850 restraints weight = 17232.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.071534 restraints weight = 13737.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.072076 restraints weight = 11646.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072351 restraints weight = 10277.100| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.7952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 5005 Z= 0.188 Angle : 0.410 3.850 6950 Z= 0.278 Chirality : 0.042 0.124 960 Planarity : 0.002 0.014 1000 Dihedral : 4.169 20.925 1000 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.62 (0.28), residues: 985 helix: 1.96 (0.20), residues: 731 sheet: None (None), residues: 0 loop : -1.65 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5005) covalent geometry : angle 0.41047 ( 6950) hydrogen bonds : bond 0.04433 ( 523) hydrogen bonds : angle 4.31693 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0236 time to fit residues: 2.7287 Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 chunk 99 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 85 optimal weight: 0.0870 chunk 83 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 overall best weight: 8.4168 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.082875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.068143 restraints weight = 23425.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.069184 restraints weight = 17349.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069832 restraints weight = 13810.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070371 restraints weight = 11763.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.070621 restraints weight = 10391.137| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.8085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 5005 Z= 0.248 Angle : 0.481 4.240 6950 Z= 0.329 Chirality : 0.043 0.126 960 Planarity : 0.003 0.015 1000 Dihedral : 4.558 21.989 1000 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.07 (0.27), residues: 985 helix: 1.60 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 130 PHE 0.000 0.000 PHE A 32 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 5005) covalent geometry : angle 0.48083 ( 6950) hydrogen bonds : bond 0.05192 ( 523) hydrogen bonds : angle 4.85294 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 699.45 seconds wall clock time: 12 minutes 36.33 seconds (756.33 seconds total)