Starting phenix.real_space_refine on Fri Feb 14 16:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckv_16703/02_2025/8ckv_16703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckv_16703/02_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_16703/02_2025/8ckv_16703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckv_16703/02_2025/8ckv_16703.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckv_16703/02_2025/8ckv_16703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckv_16703/02_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-5592/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: 4.98, per 1000 atoms: 0.50 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: 2.63 Conformation dependent library (CDL) restraints added in 1.2 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: 0.87 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: 2.64 Time building geometry restraints manager: 2.98 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.360 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.330 ------------------------------------------------------------------------------- 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= 0.283 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 *********************** 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 : 1.006 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: 1.3507 time to fit residues: 324.8214 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 : 1.147 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.167145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130389 restraints weight = 9403.610| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.73 r_work: 0.3155 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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= 0.254 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 *********************** 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 : 1.112 Fit side-chains REVERT: A 79 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: A 144 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7811 (mtp) REVERT: A 154 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7340 (mtt-85) REVERT: A 193 ASN cc_start: 0.7939 (m110) cc_final: 0.7722 (m-40) REVERT: B 144 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7962 (mtp) REVERT: C 55 MET cc_start: 0.8820 (mtp) cc_final: 0.8564 (mtp) REVERT: C 159 GLU cc_start: 0.7261 (tt0) cc_final: 0.7018 (tt0) REVERT: C 180 GLU cc_start: 0.7281 (tt0) cc_final: 0.6660 (tp30) REVERT: D 79 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: D 144 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7796 (mtp) REVERT: D 154 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7340 (mtt-85) REVERT: D 193 ASN cc_start: 0.7935 (m110) cc_final: 0.7718 (m-40) REVERT: E 144 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7972 (mtp) REVERT: F 55 MET cc_start: 0.8820 (mtp) cc_final: 0.8564 (mtp) REVERT: F 159 GLU cc_start: 0.7254 (tt0) cc_final: 0.7018 (tt0) REVERT: F 180 GLU cc_start: 0.7295 (tt0) cc_final: 0.6663 (tp30) outliers start: 24 outliers final: 4 residues processed: 156 average time/residue: 1.3478 time to fit residues: 224.5773 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 : 1.109 ------------------------------------------------------------------------------- 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 = 0.168289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131225 restraints weight = 9515.729| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.75 r_work: 0.3171 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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= 0.197 Angle : 0.491 5.292 13734 Z= 0.248 Chirality : 0.041 0.128 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.652 27.589 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: -0.14 (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 0.003 0.000 ARG D 100 *********************** 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 : 0.931 Fit side-chains REVERT: B 159 GLU cc_start: 0.7368 (tt0) cc_final: 0.7138 (tt0) REVERT: C 55 MET cc_start: 0.8783 (mtp) cc_final: 0.8570 (mtp) REVERT: C 71 GLU cc_start: 0.8201 (pt0) cc_final: 0.7962 (mt-10) REVERT: C 159 GLU cc_start: 0.7261 (tt0) cc_final: 0.6994 (tt0) REVERT: E 159 GLU cc_start: 0.7375 (tt0) cc_final: 0.7139 (tt0) REVERT: F 55 MET cc_start: 0.8788 (mtp) cc_final: 0.8576 (mtp) REVERT: F 71 GLU cc_start: 0.8215 (pt0) cc_final: 0.7972 (mt-10) REVERT: F 159 GLU cc_start: 0.7255 (tt0) cc_final: 0.6991 (tt0) outliers start: 22 outliers final: 6 residues processed: 148 average time/residue: 1.4077 time to fit residues: 222.0586 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 : 1.185 ------------------------------------------------------------------------------- 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: 0.0870 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.167731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.130698 restraints weight = 9474.135| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.75 r_work: 0.3177 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2679 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= 0.209 Angle : 0.493 5.629 13734 Z= 0.244 Chirality : 0.040 0.127 1554 Planarity : 0.005 0.038 1776 Dihedral : 4.535 27.255 1344 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 5.98 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: 1.70 (0.23), residues: 1248 helix: 1.59 (0.18), residues: 858 sheet: 0.06 (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 0.003 0.001 HIS B 120 PHE 0.011 0.002 PHE E 32 TYR 0.012 0.001 TYR C 169 ARG 0.002 0.000 ARG A 154 *********************** 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 167 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.125 Fit side-chains REVERT: A 71 GLU cc_start: 0.8303 (pt0) cc_final: 0.8079 (mt-10) REVERT: A 154 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7335 (mtt-85) REVERT: A 159 GLU cc_start: 0.7267 (tt0) cc_final: 0.7002 (tt0) REVERT: B 159 GLU cc_start: 0.7317 (tt0) cc_final: 0.7105 (tt0) REVERT: C 96 MET cc_start: 0.5548 (OUTLIER) cc_final: 0.4633 (mtt) REVERT: C 159 GLU cc_start: 0.7278 (tt0) cc_final: 0.7014 (tt0) REVERT: C 189 LEU cc_start: 0.7562 (mt) cc_final: 0.7313 (tp) REVERT: D 71 GLU cc_start: 0.8323 (pt0) cc_final: 0.8091 (mt-10) REVERT: D 154 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7342 (mtt-85) REVERT: D 159 GLU cc_start: 0.7270 (tt0) cc_final: 0.7005 (tt0) REVERT: E 159 GLU cc_start: 0.7328 (tt0) cc_final: 0.7107 (tt0) REVERT: F 96 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.4630 (mtt) REVERT: F 159 GLU cc_start: 0.7266 (tt0) cc_final: 0.7004 (tt0) REVERT: F 189 LEU cc_start: 0.7577 (mt) cc_final: 0.7326 (tp) outliers start: 30 outliers final: 6 residues processed: 155 average time/residue: 1.3340 time to fit residues: 221.6875 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 : 1.176 ------------------------------------------------------------------------------- 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: 0.0670 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.167424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129749 restraints weight = 9404.342| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.77 r_work: 0.3147 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10110 Z= 0.219 Angle : 0.495 5.933 13734 Z= 0.245 Chirality : 0.040 0.126 1554 Planarity : 0.005 0.038 1776 Dihedral : 4.476 26.509 1344 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.50 % Allowed : 11.24 % 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: 1.70 (0.23), residues: 1248 helix: 1.55 (0.18), residues: 858 sheet: 0.22 (0.57), residues: 54 loop : 0.37 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS E 120 PHE 0.010 0.002 PHE B 32 TYR 0.012 0.001 TYR F 169 ARG 0.002 0.000 ARG B 154 *********************** 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 142 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.134 Fit side-chains REVERT: A 159 GLU cc_start: 0.7157 (tt0) cc_final: 0.6899 (tt0) REVERT: A 193 ASN cc_start: 0.8184 (m110) cc_final: 0.7932 (m-40) REVERT: B 159 GLU cc_start: 0.7321 (tt0) cc_final: 0.7094 (tt0) REVERT: C 159 GLU cc_start: 0.7251 (tt0) cc_final: 0.6967 (tt0) REVERT: C 180 GLU cc_start: 0.7285 (tt0) cc_final: 0.6658 (tp30) REVERT: D 159 GLU cc_start: 0.7162 (tt0) cc_final: 0.6909 (tt0) REVERT: D 193 ASN cc_start: 0.8190 (m110) cc_final: 0.7934 (m-40) REVERT: E 159 GLU cc_start: 0.7324 (tt0) cc_final: 0.7094 (tt0) REVERT: F 159 GLU cc_start: 0.7246 (tt0) cc_final: 0.6965 (tt0) REVERT: F 180 GLU cc_start: 0.7289 (tt0) cc_final: 0.6667 (tp30) outliers start: 16 outliers final: 8 residues processed: 140 average time/residue: 1.3475 time to fit residues: 201.5335 Evaluate side-chains 134 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 75 GLU 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 75 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.167143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128927 restraints weight = 9557.572| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.79 r_work: 0.3131 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2906 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= 0.238 Angle : 0.502 5.769 13734 Z= 0.247 Chirality : 0.041 0.126 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.502 26.422 1344 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 1.63 (0.23), residues: 1248 helix: 1.47 (0.18), residues: 858 sheet: 0.36 (0.55), residues: 54 loop : 0.42 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS D 84 PHE 0.012 0.002 PHE B 32 TYR 0.013 0.001 TYR C 169 ARG 0.002 0.000 ARG C 173 *********************** 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 147 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.211 Fit side-chains REVERT: A 71 GLU cc_start: 0.8263 (pt0) cc_final: 0.7992 (mt-10) REVERT: A 154 ARG cc_start: 0.7515 (mtm-85) cc_final: 0.7167 (mtt-85) REVERT: A 193 ASN cc_start: 0.8086 (m110) cc_final: 0.7819 (m-40) REVERT: B 159 GLU cc_start: 0.7326 (tt0) cc_final: 0.7088 (tt0) REVERT: C 159 GLU cc_start: 0.7228 (tt0) cc_final: 0.6863 (tt0) REVERT: C 180 GLU cc_start: 0.7294 (tt0) cc_final: 0.6639 (tp30) REVERT: D 71 GLU cc_start: 0.8270 (pt0) cc_final: 0.7986 (mt-10) REVERT: D 154 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7160 (mtt-85) REVERT: D 193 ASN cc_start: 0.8089 (m110) cc_final: 0.7818 (m-40) REVERT: E 159 GLU cc_start: 0.7315 (tt0) cc_final: 0.7073 (tt0) REVERT: F 159 GLU cc_start: 0.7230 (tt0) cc_final: 0.6862 (tt0) REVERT: F 180 GLU cc_start: 0.7301 (tt0) cc_final: 0.6648 (tp30) outliers start: 18 outliers final: 8 residues processed: 143 average time/residue: 1.3973 time to fit residues: 213.1847 Evaluate side-chains 136 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 75 GLU 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 75 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.164944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126183 restraints weight = 9638.399| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.82 r_work: 0.3104 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2907 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= 0.315 Angle : 0.546 6.618 13734 Z= 0.269 Chirality : 0.043 0.133 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.756 27.078 1344 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.87 % Allowed : 11.33 % Favored : 86.80 % 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: 1.27 (0.23), residues: 1248 helix: 1.18 (0.17), residues: 858 sheet: 0.32 (0.50), residues: 54 loop : 0.31 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 184 HIS 0.005 0.002 HIS D 84 PHE 0.011 0.002 PHE E 32 TYR 0.015 0.002 TYR C 169 ARG 0.003 0.000 ARG C 173 *********************** 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 158 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.164 Fit side-chains REVERT: A 71 GLU cc_start: 0.8345 (pt0) cc_final: 0.8063 (mt-10) REVERT: A 154 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7191 (mtt-85) REVERT: A 193 ASN cc_start: 0.8035 (m110) cc_final: 0.7777 (m-40) REVERT: B 159 GLU cc_start: 0.7369 (tt0) cc_final: 0.7147 (tt0) REVERT: C 159 GLU cc_start: 0.7247 (tt0) cc_final: 0.6924 (tt0) REVERT: D 71 GLU cc_start: 0.8356 (pt0) cc_final: 0.8066 (mt-10) REVERT: D 154 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.7182 (mtt-85) REVERT: D 193 ASN cc_start: 0.8034 (m110) cc_final: 0.7767 (m-40) REVERT: E 159 GLU cc_start: 0.7370 (tt0) cc_final: 0.7154 (tt0) REVERT: F 159 GLU cc_start: 0.7229 (tt0) cc_final: 0.6905 (tt0) outliers start: 20 outliers final: 10 residues processed: 152 average time/residue: 1.3817 time to fit residues: 224.2038 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 : 1.127 ------------------------------------------------------------------------------- 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 83 LEU 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 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 105 optimal weight: 0.3980 chunk 85 optimal weight: 0.0020 chunk 96 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.3046 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.169569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131919 restraints weight = 9536.081| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.79 r_work: 0.3181 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3133 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= 0.165 Angle : 0.461 5.169 13734 Z= 0.227 Chirality : 0.039 0.122 1554 Planarity : 0.004 0.036 1776 Dihedral : 4.271 25.781 1344 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.06 % Allowed : 11.33 % Favored : 86.61 % 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: 1.73 (0.23), residues: 1248 helix: 1.56 (0.18), residues: 858 sheet: 0.43 (0.57), residues: 54 loop : 0.39 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 184 HIS 0.003 0.001 HIS E 120 PHE 0.012 0.002 PHE E 32 TYR 0.010 0.001 TYR C 169 ARG 0.001 0.000 ARG D 143 *********************** 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 148 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.039 Fit side-chains REVERT: A 193 ASN cc_start: 0.8059 (m110) cc_final: 0.7842 (m-40) REVERT: B 159 GLU cc_start: 0.7313 (tt0) cc_final: 0.7082 (tt0) REVERT: C 159 GLU cc_start: 0.7233 (tt0) cc_final: 0.6868 (tt0) REVERT: C 180 GLU cc_start: 0.7280 (tt0) cc_final: 0.6643 (tp30) REVERT: D 193 ASN cc_start: 0.8058 (m110) cc_final: 0.7834 (m-40) REVERT: E 159 GLU cc_start: 0.7318 (tt0) cc_final: 0.7085 (tt0) REVERT: F 159 GLU cc_start: 0.7216 (tt0) cc_final: 0.6848 (tt0) REVERT: F 180 GLU cc_start: 0.7275 (tt0) cc_final: 0.6637 (tp30) outliers start: 22 outliers final: 8 residues processed: 138 average time/residue: 1.2816 time to fit residues: 189.5148 Evaluate side-chains 130 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.166894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128442 restraints weight = 9617.848| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.81 r_work: 0.3129 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3095 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= 0.251 Angle : 0.509 7.675 13734 Z= 0.249 Chirality : 0.041 0.126 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.467 25.967 1344 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.50 % Allowed : 12.27 % Favored : 86.24 % 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: 1.40 (0.18), residues: 858 sheet: 0.37 (0.55), residues: 54 loop : 0.37 (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 D 84 PHE 0.011 0.002 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG A 154 *********************** 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 145 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.188 Fit side-chains REVERT: A 71 GLU cc_start: 0.8286 (pt0) cc_final: 0.8005 (mt-10) REVERT: A 193 ASN cc_start: 0.8031 (m110) cc_final: 0.7787 (m-40) REVERT: B 159 GLU cc_start: 0.7355 (tt0) cc_final: 0.7108 (tt0) REVERT: C 159 GLU cc_start: 0.7269 (tt0) cc_final: 0.6907 (tt0) REVERT: D 71 GLU cc_start: 0.8290 (pt0) cc_final: 0.8005 (mt-10) REVERT: D 193 ASN cc_start: 0.8034 (m110) cc_final: 0.7783 (m-40) REVERT: E 159 GLU cc_start: 0.7348 (tt0) cc_final: 0.7103 (tt0) REVERT: F 159 GLU cc_start: 0.7247 (tt0) cc_final: 0.6884 (tt0) outliers start: 16 outliers final: 10 residues processed: 141 average time/residue: 1.3591 time to fit residues: 205.3144 Evaluate side-chains 138 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 109 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.169042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131447 restraints weight = 9469.834| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.77 r_work: 0.3167 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3211 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= 0.181 Angle : 0.481 9.343 13734 Z= 0.234 Chirality : 0.040 0.123 1554 Planarity : 0.004 0.036 1776 Dihedral : 4.242 25.264 1344 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.94 % Allowed : 12.92 % Favored : 86.14 % 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: 1.73 (0.23), residues: 1248 helix: 1.55 (0.18), residues: 858 sheet: 0.34 (0.58), residues: 54 loop : 0.43 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 184 HIS 0.003 0.001 HIS F 120 PHE 0.011 0.002 PHE E 32 TYR 0.011 0.001 TYR F 169 ARG 0.002 0.000 ARG D 154 ********************** 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 134 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.127 Fit side-chains REVERT: A 154 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7060 (mtt-85) REVERT: A 193 ASN cc_start: 0.8061 (m110) cc_final: 0.7774 (m-40) REVERT: B 159 GLU cc_start: 0.7301 (tt0) cc_final: 0.7066 (tt0) REVERT: C 159 GLU cc_start: 0.7213 (tt0) cc_final: 0.6875 (tt0) REVERT: C 180 GLU cc_start: 0.7255 (tt0) cc_final: 0.6600 (tp30) REVERT: D 154 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7059 (mtt-85) REVERT: D 193 ASN cc_start: 0.8066 (m110) cc_final: 0.7777 (m-40) REVERT: E 159 GLU cc_start: 0.7306 (tt0) cc_final: 0.7066 (tt0) REVERT: F 159 GLU cc_start: 0.7191 (tt0) cc_final: 0.6853 (tt0) REVERT: F 180 GLU cc_start: 0.7246 (tt0) cc_final: 0.6600 (tp30) outliers start: 10 outliers final: 8 residues processed: 132 average time/residue: 1.4223 time to fit residues: 200.1380 Evaluate side-chains 130 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.167233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.128509 restraints weight = 9568.510| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.82 r_work: 0.3125 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3158 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= 0.248 Angle : 0.519 9.966 13734 Z= 0.251 Chirality : 0.041 0.126 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.418 25.471 1344 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.31 % Allowed : 12.55 % Favored : 86.14 % 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: 0.27 (0.56), residues: 54 loop : 0.42 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS D 84 PHE 0.011 0.002 PHE E 32 TYR 0.013 0.001 TYR C 169 ARG 0.002 0.000 ARG F 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7317.28 seconds wall clock time: 130 minutes 18.70 seconds (7818.70 seconds total)