Starting phenix.real_space_refine on Mon Jul 28 14:33:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckv_16703/07_2025/8ckv_16703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckv_16703/07_2025/8ckv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ckv_16703/07_2025/8ckv_16703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckv_16703/07_2025/8ckv_16703.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckv_16703/07_2025/8ckv_16703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckv_16703/07_2025/8ckv_16703.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 4.85, per 1000 atoms: 0.49 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.91 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: 3.38 Time building geometry restraints manager: 2.89 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 11.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:20.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.004 TRP F 117 HIS 0.012 0.005 HIS A 12 PHE 0.011 0.003 PHE E 40 TYR 0.018 0.005 TYR D 145 ARG 0.016 0.003 ARG C 97 Details of bonding type rmsd hydrogen bonds : bond 0.10966 ( 618) hydrogen bonds : angle 6.41310 ( 1818) covalent geometry : bond 0.00449 (10110) covalent geometry : angle 0.82293 (13734) *********************** 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 : 1.081 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: 1.3502 time to fit residues: 324.6449 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 : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 38 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.167186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.130539 restraints weight = 9402.680| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.73 r_work: 0.3155 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10110 Z= 0.156 Angle : 0.558 5.410 13734 Z= 0.285 Chirality : 0.042 0.127 1554 Planarity : 0.006 0.076 1776 Dihedral : 5.185 29.475 1344 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.25 % Allowed : 6.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1248 helix: 1.30 (0.17), residues: 858 sheet: -0.16 (0.50), residues: 54 loop : 0.14 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 117 HIS 0.003 0.001 HIS B 120 PHE 0.011 0.002 PHE E 32 TYR 0.012 0.002 TYR A 169 ARG 0.004 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 618) hydrogen bonds : angle 4.23419 ( 1818) covalent geometry : bond 0.00389 (10110) covalent geometry : angle 0.55791 (13734) *********************** 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 168 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.132 Fit side-chains REVERT: A 79 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: A 144 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7828 (mtp) REVERT: A 154 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7363 (mtt-85) REVERT: A 193 ASN cc_start: 0.7949 (m110) cc_final: 0.7732 (m-40) REVERT: B 144 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7976 (mtp) REVERT: C 55 MET cc_start: 0.8830 (mtp) cc_final: 0.8575 (mtp) REVERT: C 159 GLU cc_start: 0.7262 (tt0) cc_final: 0.7029 (tt0) REVERT: C 180 GLU cc_start: 0.7299 (tt0) cc_final: 0.6686 (tp30) REVERT: D 79 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6479 (mt-10) REVERT: D 144 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7812 (mtp) REVERT: D 154 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7362 (mtt-85) REVERT: D 193 ASN cc_start: 0.7946 (m110) cc_final: 0.7728 (m-40) REVERT: E 144 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7985 (mtp) REVERT: F 55 MET cc_start: 0.8831 (mtp) cc_final: 0.8576 (mtp) REVERT: F 159 GLU cc_start: 0.7254 (tt0) cc_final: 0.7030 (tt0) REVERT: F 180 GLU cc_start: 0.7314 (tt0) cc_final: 0.6689 (tp30) outliers start: 24 outliers final: 4 residues processed: 156 average time/residue: 1.3032 time to fit residues: 217.0441 Evaluate side-chains 144 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU 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 D residue 79 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 95 optimal weight: 0.0170 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.168291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131217 restraints weight = 9515.195| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.75 r_work: 0.3178 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10110 Z= 0.123 Angle : 0.491 5.291 13734 Z= 0.248 Chirality : 0.041 0.128 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.652 27.586 1344 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.06 % Allowed : 7.49 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1248 helix: 1.63 (0.18), residues: 858 sheet: -0.13 (0.56), residues: 54 loop : 0.38 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.003 0.001 HIS D 120 PHE 0.011 0.002 PHE E 32 TYR 0.011 0.001 TYR F 169 ARG 0.002 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 618) hydrogen bonds : angle 3.78789 ( 1818) covalent geometry : bond 0.00301 (10110) covalent geometry : angle 0.49143 (13734) *********************** 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 152 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.202 Fit side-chains REVERT: B 159 GLU cc_start: 0.7384 (tt0) cc_final: 0.7162 (tt0) REVERT: C 55 MET cc_start: 0.8795 (mtp) cc_final: 0.8583 (mtp) REVERT: C 71 GLU cc_start: 0.8214 (pt0) cc_final: 0.7988 (mt-10) REVERT: C 159 GLU cc_start: 0.7269 (tt0) cc_final: 0.7018 (tt0) REVERT: E 159 GLU cc_start: 0.7388 (tt0) cc_final: 0.7161 (tt0) REVERT: F 55 MET cc_start: 0.8800 (mtp) cc_final: 0.8589 (mtp) REVERT: F 71 GLU cc_start: 0.8224 (pt0) cc_final: 0.7997 (mt-10) REVERT: F 159 GLU cc_start: 0.7262 (tt0) cc_final: 0.7016 (tt0) outliers start: 22 outliers final: 6 residues processed: 148 average time/residue: 1.3707 time to fit residues: 216.2334 Evaluate side-chains 125 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 83 LEU 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 122 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.167666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131696 restraints weight = 9461.102| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.69 r_work: 0.3168 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10110 Z= 0.133 Angle : 0.499 5.609 13734 Z= 0.247 Chirality : 0.041 0.128 1554 Planarity : 0.005 0.038 1776 Dihedral : 4.563 27.282 1344 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.81 % Allowed : 8.43 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.23), residues: 1248 helix: 1.55 (0.18), residues: 858 sheet: 0.09 (0.58), residues: 54 loop : 0.28 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.004 0.001 HIS B 120 PHE 0.011 0.002 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 618) hydrogen bonds : angle 3.75815 ( 1818) covalent geometry : bond 0.00331 (10110) covalent geometry : angle 0.49855 (13734) *********************** 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 169 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.014 Fit side-chains REVERT: A 71 GLU cc_start: 0.8321 (pt0) cc_final: 0.8099 (mt-10) REVERT: A 154 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7373 (mtt-85) REVERT: A 159 GLU cc_start: 0.7194 (tt0) cc_final: 0.6989 (tt0) REVERT: B 159 GLU cc_start: 0.7331 (tt0) cc_final: 0.7121 (tt0) REVERT: C 96 MET cc_start: 0.5600 (OUTLIER) cc_final: 0.4673 (mtt) REVERT: C 159 GLU cc_start: 0.7286 (tt0) cc_final: 0.7038 (tt0) REVERT: C 180 GLU cc_start: 0.7329 (tt0) cc_final: 0.6758 (tp30) REVERT: D 71 GLU cc_start: 0.8331 (pt0) cc_final: 0.8102 (mt-10) REVERT: D 154 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7376 (mtt-85) REVERT: D 159 GLU cc_start: 0.7201 (tt0) cc_final: 0.6993 (tt0) REVERT: E 159 GLU cc_start: 0.7337 (tt0) cc_final: 0.7123 (tt0) REVERT: F 96 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.4674 (mtt) REVERT: F 159 GLU cc_start: 0.7277 (tt0) cc_final: 0.7032 (tt0) REVERT: F 180 GLU cc_start: 0.7340 (tt0) cc_final: 0.6770 (tp30) outliers start: 30 outliers final: 6 residues processed: 157 average time/residue: 1.2738 time to fit residues: 213.6582 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 : 1.003 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain C residue 96 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 Chi-restraints excluded: chain F residue 96 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN C 193 ASN E 193 ASN F 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.128862 restraints weight = 9435.375| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.77 r_work: 0.3140 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10110 Z= 0.143 Angle : 0.506 6.004 13734 Z= 0.250 Chirality : 0.041 0.128 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.547 26.632 1344 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.25 % Allowed : 10.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.23), residues: 1248 helix: 1.49 (0.18), residues: 858 sheet: 0.28 (0.56), residues: 54 loop : 0.31 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.003 0.001 HIS E 120 PHE 0.011 0.002 PHE E 32 TYR 0.013 0.001 TYR C 169 ARG 0.002 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 618) hydrogen bonds : angle 3.78186 ( 1818) covalent geometry : bond 0.00359 (10110) covalent geometry : angle 0.50627 (13734) *********************** 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 152 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.131 Fit side-chains REVERT: A 71 GLU cc_start: 0.8282 (pt0) cc_final: 0.8026 (mt-10) REVERT: A 154 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7233 (mtt-85) REVERT: A 159 GLU cc_start: 0.7204 (tt0) cc_final: 0.6818 (tt0) REVERT: A 193 ASN cc_start: 0.8222 (m110) cc_final: 0.7928 (m-40) REVERT: B 159 GLU cc_start: 0.7342 (tt0) cc_final: 0.7133 (tt0) REVERT: C 159 GLU cc_start: 0.7265 (tt0) cc_final: 0.7006 (tt0) REVERT: C 180 GLU cc_start: 0.7341 (tt0) cc_final: 0.6719 (tp30) REVERT: D 71 GLU cc_start: 0.8296 (pt0) cc_final: 0.8033 (mt-10) REVERT: D 154 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7225 (mtt-85) REVERT: D 159 GLU cc_start: 0.7200 (tt0) cc_final: 0.6814 (tt0) REVERT: D 193 ASN cc_start: 0.8225 (m110) cc_final: 0.7918 (m-40) REVERT: E 159 GLU cc_start: 0.7336 (tt0) cc_final: 0.7127 (tt0) REVERT: F 159 GLU cc_start: 0.7257 (tt0) cc_final: 0.6998 (tt0) REVERT: F 180 GLU cc_start: 0.7345 (tt0) cc_final: 0.6723 (tp30) outliers start: 24 outliers final: 12 residues processed: 142 average time/residue: 1.3025 time to fit residues: 198.1768 Evaluate side-chains 138 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 75 GLU 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 122 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 ASN F 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.168221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.131231 restraints weight = 9533.018| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.74 r_work: 0.3156 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2956 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= 0.125 Angle : 0.480 5.673 13734 Z= 0.236 Chirality : 0.040 0.123 1554 Planarity : 0.005 0.038 1776 Dihedral : 4.378 26.138 1344 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.87 % Allowed : 11.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.23), residues: 1248 helix: 1.55 (0.18), residues: 858 sheet: 0.45 (0.57), residues: 54 loop : 0.39 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.003 0.001 HIS C 120 PHE 0.010 0.002 PHE B 32 TYR 0.012 0.001 TYR C 169 ARG 0.002 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 618) hydrogen bonds : angle 3.70954 ( 1818) covalent geometry : bond 0.00311 (10110) covalent geometry : angle 0.48001 (13734) *********************** 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 144 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.101 Fit side-chains REVERT: A 159 GLU cc_start: 0.7096 (tt0) cc_final: 0.6877 (tt0) REVERT: A 193 ASN cc_start: 0.8115 (m110) cc_final: 0.7866 (m-40) REVERT: B 159 GLU cc_start: 0.7340 (tt0) cc_final: 0.7131 (tt0) REVERT: C 159 GLU cc_start: 0.7238 (tt0) cc_final: 0.6969 (tt0) REVERT: C 180 GLU cc_start: 0.7273 (tt0) cc_final: 0.6663 (tp30) REVERT: D 159 GLU cc_start: 0.7100 (tt0) cc_final: 0.6881 (tt0) REVERT: D 193 ASN cc_start: 0.8124 (m110) cc_final: 0.7871 (m-40) REVERT: E 159 GLU cc_start: 0.7333 (tt0) cc_final: 0.7121 (tt0) REVERT: F 159 GLU cc_start: 0.7225 (tt0) cc_final: 0.6954 (tt0) REVERT: F 180 GLU cc_start: 0.7281 (tt0) cc_final: 0.6667 (tp30) outliers start: 20 outliers final: 6 residues processed: 138 average time/residue: 1.3708 time to fit residues: 201.9559 Evaluate side-chains 128 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.166309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127823 restraints weight = 9592.786| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.81 r_work: 0.3118 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10110 Z= 0.156 Angle : 0.510 6.465 13734 Z= 0.251 Chirality : 0.041 0.127 1554 Planarity : 0.005 0.038 1776 Dihedral : 4.549 26.353 1344 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.69 % Allowed : 11.05 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1248 helix: 1.37 (0.18), residues: 858 sheet: 0.47 (0.54), residues: 54 loop : 0.38 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.003 0.002 HIS D 84 PHE 0.010 0.002 PHE B 32 TYR 0.014 0.001 TYR C 169 ARG 0.002 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 618) hydrogen bonds : angle 3.81692 ( 1818) covalent geometry : bond 0.00396 (10110) covalent geometry : angle 0.51031 (13734) *********************** 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 152 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.053 Fit side-chains REVERT: A 71 GLU cc_start: 0.8288 (pt0) cc_final: 0.8000 (mt-10) REVERT: A 159 GLU cc_start: 0.7144 (tt0) cc_final: 0.6850 (tt0) REVERT: A 193 ASN cc_start: 0.8063 (m110) cc_final: 0.7822 (m-40) REVERT: B 159 GLU cc_start: 0.7355 (tt0) cc_final: 0.7115 (tt0) REVERT: C 159 GLU cc_start: 0.7263 (tt0) cc_final: 0.6896 (tt0) REVERT: D 71 GLU cc_start: 0.8303 (pt0) cc_final: 0.8006 (mt-10) REVERT: D 159 GLU cc_start: 0.7145 (tt0) cc_final: 0.6844 (tt0) REVERT: D 193 ASN cc_start: 0.8062 (m110) cc_final: 0.7815 (m-40) REVERT: E 159 GLU cc_start: 0.7354 (tt0) cc_final: 0.7115 (tt0) REVERT: F 159 GLU cc_start: 0.7252 (tt0) cc_final: 0.6883 (tt0) outliers start: 18 outliers final: 8 residues processed: 146 average time/residue: 1.3567 time to fit residues: 211.4610 Evaluate side-chains 138 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 C residue 146 SER 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 146 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.0060 chunk 96 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.168816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130303 restraints weight = 9564.501| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.82 r_work: 0.3156 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3106 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 6.465 13734 Z= 0.231 Chirality : 0.040 0.122 1554 Planarity : 0.004 0.037 1776 Dihedral : 4.277 25.526 1344 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.87 % Allowed : 12.36 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.23), residues: 1248 helix: 1.58 (0.18), residues: 858 sheet: 0.47 (0.58), residues: 54 loop : 0.45 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.003 0.001 HIS C 120 PHE 0.012 0.002 PHE B 32 TYR 0.011 0.001 TYR C 169 ARG 0.002 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 618) hydrogen bonds : angle 3.67217 ( 1818) covalent geometry : bond 0.00278 (10110) covalent geometry : angle 0.47363 (13734) *********************** 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 150 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.007 Fit side-chains REVERT: A 71 GLU cc_start: 0.8225 (pt0) cc_final: 0.7961 (mt-10) REVERT: A 159 GLU cc_start: 0.6916 (tt0) cc_final: 0.6693 (tt0) REVERT: A 193 ASN cc_start: 0.8053 (m110) cc_final: 0.7822 (m-40) REVERT: B 159 GLU cc_start: 0.7316 (tt0) cc_final: 0.7083 (tt0) REVERT: B 192 GLN cc_start: 0.7269 (mt0) cc_final: 0.7060 (tt0) REVERT: C 159 GLU cc_start: 0.7250 (tt0) cc_final: 0.6892 (tt0) REVERT: C 180 GLU cc_start: 0.7212 (tt0) cc_final: 0.6554 (tp30) REVERT: D 71 GLU cc_start: 0.8236 (pt0) cc_final: 0.7963 (mt-10) REVERT: D 159 GLU cc_start: 0.6914 (tt0) cc_final: 0.6692 (tt0) REVERT: D 193 ASN cc_start: 0.8060 (m110) cc_final: 0.7824 (m-40) REVERT: E 159 GLU cc_start: 0.7315 (tt0) cc_final: 0.7083 (tt0) REVERT: E 192 GLN cc_start: 0.7282 (mt0) cc_final: 0.7074 (tt0) REVERT: F 159 GLU cc_start: 0.7229 (tt0) cc_final: 0.6873 (tt0) REVERT: F 180 GLU cc_start: 0.7212 (tt0) cc_final: 0.6553 (tp30) outliers start: 20 outliers final: 10 residues processed: 142 average time/residue: 1.3799 time to fit residues: 209.4329 Evaluate side-chains 134 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 146 SER 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 146 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.165348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126524 restraints weight = 9616.996| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.82 r_work: 0.3101 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3035 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= 0.185 Angle : 0.544 7.985 13734 Z= 0.265 Chirality : 0.043 0.130 1554 Planarity : 0.005 0.038 1776 Dihedral : 4.642 26.416 1344 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.69 % Allowed : 12.55 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1248 helix: 1.24 (0.18), residues: 858 sheet: 0.32 (0.52), residues: 54 loop : 0.40 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.005 0.002 HIS A 84 PHE 0.010 0.002 PHE B 32 TYR 0.014 0.002 TYR F 169 ARG 0.002 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 618) hydrogen bonds : angle 3.90946 ( 1818) covalent geometry : bond 0.00472 (10110) covalent geometry : angle 0.54381 (13734) *********************** 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 152 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 2.104 Fit side-chains REVERT: A 71 GLU cc_start: 0.8338 (pt0) cc_final: 0.8055 (mt-10) REVERT: A 159 GLU cc_start: 0.7088 (tt0) cc_final: 0.6761 (tt0) REVERT: A 193 ASN cc_start: 0.8028 (m110) cc_final: 0.7797 (m-40) REVERT: B 159 GLU cc_start: 0.7373 (tt0) cc_final: 0.7132 (tt0) REVERT: C 159 GLU cc_start: 0.7289 (tt0) cc_final: 0.6949 (tt0) REVERT: D 71 GLU cc_start: 0.8345 (pt0) cc_final: 0.8056 (mt-10) REVERT: D 159 GLU cc_start: 0.7087 (tt0) cc_final: 0.6756 (tt0) REVERT: D 193 ASN cc_start: 0.8031 (m110) cc_final: 0.7796 (m-40) REVERT: E 159 GLU cc_start: 0.7363 (tt0) cc_final: 0.7121 (tt0) REVERT: F 159 GLU cc_start: 0.7278 (tt0) cc_final: 0.6936 (tt0) outliers start: 18 outliers final: 12 residues processed: 148 average time/residue: 1.6862 time to fit residues: 268.1722 Evaluate side-chains 144 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE 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 146 SER Chi-restraints excluded: chain D 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 Chi-restraints excluded: chain F residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.167943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131219 restraints weight = 9476.211| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.73 r_work: 0.3153 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10110 Z= 0.126 Angle : 0.493 7.308 13734 Z= 0.240 Chirality : 0.041 0.124 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.375 25.853 1344 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.50 % Allowed : 12.55 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1248 helix: 1.44 (0.18), residues: 858 sheet: 0.38 (0.56), residues: 54 loop : 0.44 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.003 0.001 HIS A 120 PHE 0.012 0.002 PHE E 32 TYR 0.012 0.001 TYR B 169 ARG 0.002 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 618) hydrogen bonds : angle 3.76261 ( 1818) covalent geometry : bond 0.00311 (10110) covalent geometry : angle 0.49279 (13734) ********************** 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 144 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.000 Fit side-chains REVERT: A 71 GLU cc_start: 0.8298 (pt0) cc_final: 0.8058 (mt-10) REVERT: A 193 ASN cc_start: 0.8099 (m110) cc_final: 0.7858 (m-40) REVERT: B 159 GLU cc_start: 0.7367 (tt0) cc_final: 0.7153 (tt0) REVERT: C 159 GLU cc_start: 0.7276 (tt0) cc_final: 0.6955 (tt0) REVERT: D 71 GLU cc_start: 0.8306 (pt0) cc_final: 0.8060 (mt-10) REVERT: D 193 ASN cc_start: 0.8101 (m110) cc_final: 0.7857 (m-40) REVERT: E 159 GLU cc_start: 0.7370 (tt0) cc_final: 0.7155 (tt0) REVERT: F 159 GLU cc_start: 0.7255 (tt0) cc_final: 0.6936 (tt0) outliers start: 16 outliers final: 10 residues processed: 140 average time/residue: 1.3405 time to fit residues: 200.5155 Evaluate side-chains 132 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 146 SER 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 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 114 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.167568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129285 restraints weight = 9555.245| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.80 r_work: 0.3132 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10110 Z= 0.141 Angle : 0.517 9.593 13734 Z= 0.250 Chirality : 0.041 0.125 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.416 25.579 1344 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.50 % Allowed : 12.55 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1248 helix: 1.39 (0.18), residues: 858 sheet: 0.34 (0.54), residues: 54 loop : 0.40 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.003 0.001 HIS A 84 PHE 0.011 0.002 PHE B 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 618) hydrogen bonds : angle 3.79598 ( 1818) covalent geometry : bond 0.00353 (10110) covalent geometry : angle 0.51678 (13734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7510.75 seconds wall clock time: 131 minutes 43.45 seconds (7903.45 seconds total)