Starting phenix.real_space_refine on Wed Sep 17 18:40:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h3f_51819/09_2025/9h3f_51819.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h3f_51819/09_2025/9h3f_51819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h3f_51819/09_2025/9h3f_51819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h3f_51819/09_2025/9h3f_51819.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h3f_51819/09_2025/9h3f_51819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h3f_51819/09_2025/9h3f_51819.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 12 5.21 5 S 60 5.16 5 C 6534 2.51 5 N 1710 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10212 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1700 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "B" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1700 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "C" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1700 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "D" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1700 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "E" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1700 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1700 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.73, per 1000 atoms: 0.27 Number of scatterers: 10212 At special positions: 0 Unit cell: (113.63, 106.528, 68.6517, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 12 11.99 O 1896 8.00 N 1710 7.00 C 6534 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: 1.00 Conformation dependent library (CDL) restraints added in 379.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 67.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.518A pdb=" N MET A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 123 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 Processing helix chain 'A' and resid 139 through 146 Processing helix chain 'A' and resid 158 through 178 Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.693A pdb=" N MET A 222 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 removed outlier: 4.089A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 264 through 287 removed outlier: 3.698A pdb=" N LEU A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.688A pdb=" N MET B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 158 through 178 Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.540A pdb=" N MET B 222 " --> pdb=" O HIS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 removed outlier: 4.160A pdb=" N LEU B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 264 through 287 removed outlier: 3.589A pdb=" N LEU B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 125 through 139 Processing helix chain 'C' and resid 139 through 146 Processing helix chain 'C' and resid 158 through 178 removed outlier: 3.545A pdb=" N TYR C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.556A pdb=" N LEU C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.506A pdb=" N ILE C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET C 222 " --> pdb=" O HIS C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 removed outlier: 4.121A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 264 through 287 Processing helix chain 'D' and resid 108 through 122 removed outlier: 3.550A pdb=" N MET D 112 " --> pdb=" O PRO D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 139 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 158 through 178 Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 210 through 216 Processing helix chain 'D' and resid 217 through 233 removed outlier: 3.624A pdb=" N MET D 222 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 4.076A pdb=" N LEU D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 264 through 287 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'E' and resid 125 through 139 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 158 through 178 Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.515A pdb=" N LEU E 201 " --> pdb=" O LYS E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 217 through 233 removed outlier: 3.594A pdb=" N MET E 222 " --> pdb=" O HIS E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 249 removed outlier: 4.132A pdb=" N LEU E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 264 through 287 Processing helix chain 'F' and resid 108 through 122 removed outlier: 3.593A pdb=" N MET F 112 " --> pdb=" O PRO F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 139 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 158 through 178 Processing helix chain 'F' and resid 182 through 193 Processing helix chain 'F' and resid 196 through 201 Processing helix chain 'F' and resid 210 through 216 Processing helix chain 'F' and resid 217 through 233 removed outlier: 3.784A pdb=" N MET F 222 " --> pdb=" O HIS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 249 removed outlier: 4.076A pdb=" N LEU F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 264 through 287 578 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3307 1.34 - 1.46: 2007 1.46 - 1.58: 5000 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 10434 Sorted by residual: bond pdb=" CG LEU C 168 " pdb=" CD1 LEU C 168 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" CB MET C 167 " pdb=" CG MET C 167 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CG LEU F 168 " pdb=" CD1 LEU F 168 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CB VAL C 190 " pdb=" CG1 VAL C 190 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.24e+00 bond pdb=" CB VAL F 190 " pdb=" CG1 VAL F 190 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 ... (remaining 10429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 13840 2.77 - 5.55: 237 5.55 - 8.32: 27 8.32 - 11.10: 5 11.10 - 13.87: 3 Bond angle restraints: 14112 Sorted by residual: angle pdb=" CB MET E 283 " pdb=" CG MET E 283 " pdb=" SD MET E 283 " ideal model delta sigma weight residual 112.70 98.83 13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CB MET D 283 " pdb=" CG MET D 283 " pdb=" SD MET D 283 " ideal model delta sigma weight residual 112.70 100.46 12.24 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CB MET A 283 " pdb=" CG MET A 283 " pdb=" SD MET A 283 " ideal model delta sigma weight residual 112.70 101.00 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB MET C 167 " pdb=" CG MET C 167 " pdb=" SD MET C 167 " ideal model delta sigma weight residual 112.70 101.95 10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C LYS D 151 " pdb=" N ASN D 152 " pdb=" CA ASN D 152 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 ... (remaining 14107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5695 17.73 - 35.47: 558 35.47 - 53.20: 106 53.20 - 70.93: 16 70.93 - 88.67: 3 Dihedral angle restraints: 6378 sinusoidal: 2622 harmonic: 3756 Sorted by residual: dihedral pdb=" CA PRO B 108 " pdb=" C PRO B 108 " pdb=" N LYS B 109 " pdb=" CA LYS B 109 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PRO F 108 " pdb=" C PRO F 108 " pdb=" N LYS F 109 " pdb=" CA LYS F 109 " ideal model delta harmonic sigma weight residual -180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PRO C 108 " pdb=" C PRO C 108 " pdb=" N LYS C 109 " pdb=" CA LYS C 109 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 6375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 993 0.044 - 0.087: 425 0.087 - 0.131: 125 0.131 - 0.174: 30 0.174 - 0.218: 5 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CG LEU B 215 " pdb=" CB LEU B 215 " pdb=" CD1 LEU B 215 " pdb=" CD2 LEU B 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU A 215 " pdb=" CB LEU A 215 " pdb=" CD1 LEU A 215 " pdb=" CD2 LEU A 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU D 215 " pdb=" CB LEU D 215 " pdb=" CD1 LEU D 215 " pdb=" CD2 LEU D 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1575 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 266 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" CD GLU B 266 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 266 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 266 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 266 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" CD GLU C 266 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU C 266 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 266 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 266 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" CD GLU A 266 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU A 266 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 266 " 0.012 2.00e-02 2.50e+03 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 45 2.56 - 3.15: 7859 3.15 - 3.73: 16011 3.73 - 4.32: 21002 4.32 - 4.90: 35440 Nonbonded interactions: 80357 Sorted by model distance: nonbonded pdb=" OD2 ASP F 194 " pdb="MG MG F1002 " model vdw 1.976 2.170 nonbonded pdb=" OD2 ASP A 194 " pdb="MG MG A1002 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP F 274 " pdb="MG MG F1002 " model vdw 2.025 2.170 nonbonded pdb=" OD1 ASP A 274 " pdb="MG MG A1002 " model vdw 2.042 2.170 nonbonded pdb=" OD2 ASP D 194 " pdb="MG MG D1002 " model vdw 2.049 2.170 ... (remaining 80352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.940 Find NCS groups from input model: 0.220 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10434 Z= 0.208 Angle : 0.878 13.871 14112 Z= 0.444 Chirality : 0.053 0.218 1578 Planarity : 0.006 0.040 1800 Dihedral : 14.322 88.668 3942 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.22), residues: 1260 helix: -0.27 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.42 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 285 TYR 0.019 0.002 TYR A 178 PHE 0.026 0.003 PHE B 143 TRP 0.001 0.000 TRP E 256 HIS 0.015 0.003 HIS F 250 Details of bonding type rmsd covalent geometry : bond 0.00488 (10434) covalent geometry : angle 0.87814 (14112) hydrogen bonds : bond 0.16417 ( 578) hydrogen bonds : angle 6.05139 ( 1698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.402 Fit side-chains REVERT: B 263 MET cc_start: 0.7654 (mtt) cc_final: 0.6908 (mtm) REVERT: C 280 MET cc_start: 0.7114 (tpp) cc_final: 0.6679 (tpt) REVERT: D 280 MET cc_start: 0.7367 (tpp) cc_final: 0.7085 (mmm) REVERT: D 294 GLU cc_start: 0.7937 (tt0) cc_final: 0.7300 (mt-10) REVERT: E 112 MET cc_start: 0.5806 (mtt) cc_final: 0.5501 (mtp) REVERT: E 263 MET cc_start: 0.7311 (mtt) cc_final: 0.6832 (mtm) REVERT: E 294 GLU cc_start: 0.7642 (tt0) cc_final: 0.7105 (mt-10) REVERT: F 294 GLU cc_start: 0.7683 (tt0) cc_final: 0.6999 (mt-10) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0922 time to fit residues: 13.5466 Evaluate side-chains 92 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 244 GLN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS C 163 HIS C 245 HIS ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS E 244 GLN F 129 GLN F 139 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.210229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.182159 restraints weight = 80189.861| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 6.58 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10434 Z= 0.167 Angle : 0.636 14.441 14112 Z= 0.316 Chirality : 0.043 0.128 1578 Planarity : 0.004 0.036 1800 Dihedral : 4.299 19.065 1362 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.53 % Allowed : 6.95 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.23), residues: 1260 helix: 0.38 (0.17), residues: 792 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 133 TYR 0.012 0.001 TYR A 178 PHE 0.015 0.002 PHE A 143 TRP 0.006 0.001 TRP A 256 HIS 0.009 0.002 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00410 (10434) covalent geometry : angle 0.63616 (14112) hydrogen bonds : bond 0.04767 ( 578) hydrogen bonds : angle 4.41315 ( 1698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.319 Fit side-chains REVERT: C 280 MET cc_start: 0.7309 (tpp) cc_final: 0.7066 (tpp) REVERT: D 294 GLU cc_start: 0.7312 (tt0) cc_final: 0.7047 (mt-10) REVERT: E 112 MET cc_start: 0.6393 (mtt) cc_final: 0.6188 (mtt) REVERT: E 225 GLU cc_start: 0.7284 (tp30) cc_final: 0.6673 (mm-30) REVERT: F 283 MET cc_start: 0.6368 (ttm) cc_final: 0.5975 (ttm) outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 0.0820 time to fit residues: 11.8347 Evaluate side-chains 91 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain F residue 282 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.208114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.180518 restraints weight = 81544.331| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 6.60 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10434 Z= 0.133 Angle : 0.556 12.821 14112 Z= 0.274 Chirality : 0.041 0.137 1578 Planarity : 0.004 0.037 1800 Dihedral : 4.042 18.320 1362 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.34 % Allowed : 9.98 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.23), residues: 1260 helix: 0.86 (0.18), residues: 798 sheet: None (None), residues: 0 loop : -0.11 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 285 TYR 0.013 0.001 TYR A 178 PHE 0.012 0.001 PHE E 143 TRP 0.001 0.000 TRP A 256 HIS 0.007 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00316 (10434) covalent geometry : angle 0.55619 (14112) hydrogen bonds : bond 0.04104 ( 578) hydrogen bonds : angle 4.21764 ( 1698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.418 Fit side-chains REVERT: C 280 MET cc_start: 0.7250 (tpp) cc_final: 0.6951 (tpp) REVERT: E 225 GLU cc_start: 0.7192 (tp30) cc_final: 0.6566 (mm-30) REVERT: F 280 MET cc_start: 0.6892 (tpp) cc_final: 0.6447 (tpt) outliers start: 15 outliers final: 5 residues processed: 95 average time/residue: 0.0824 time to fit residues: 12.4053 Evaluate side-chains 91 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.251954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.204925 restraints weight = 88851.632| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 8.90 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10434 Z= 0.141 Angle : 0.553 12.385 14112 Z= 0.273 Chirality : 0.041 0.153 1578 Planarity : 0.004 0.036 1800 Dihedral : 3.929 16.144 1362 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.78 % Allowed : 10.87 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.23), residues: 1260 helix: 1.11 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.07 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 133 TYR 0.012 0.001 TYR E 272 PHE 0.014 0.001 PHE F 143 TRP 0.003 0.000 TRP D 256 HIS 0.006 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00342 (10434) covalent geometry : angle 0.55257 (14112) hydrogen bonds : bond 0.03996 ( 578) hydrogen bonds : angle 4.15306 ( 1698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.418 Fit side-chains REVERT: A 263 MET cc_start: 0.7461 (mtt) cc_final: 0.7013 (mtp) REVERT: A 297 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6386 (pm20) REVERT: B 263 MET cc_start: 0.7610 (mtt) cc_final: 0.7113 (mtp) REVERT: C 280 MET cc_start: 0.6720 (tpp) cc_final: 0.6203 (tpt) REVERT: E 222 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8360 (tpp) REVERT: E 225 GLU cc_start: 0.7291 (tp30) cc_final: 0.6426 (mm-30) REVERT: F 263 MET cc_start: 0.7515 (mtt) cc_final: 0.7235 (mtt) REVERT: F 297 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.5815 (mp0) outliers start: 20 outliers final: 5 residues processed: 95 average time/residue: 0.0802 time to fit residues: 12.2397 Evaluate side-chains 88 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 297 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS F 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.248142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.201950 restraints weight = 90083.138| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 9.11 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10434 Z= 0.150 Angle : 0.551 11.697 14112 Z= 0.273 Chirality : 0.041 0.144 1578 Planarity : 0.004 0.034 1800 Dihedral : 3.863 16.065 1362 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.14 % Allowed : 11.59 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.23), residues: 1260 helix: 1.11 (0.18), residues: 798 sheet: -1.49 (0.55), residues: 60 loop : 0.06 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 133 TYR 0.013 0.001 TYR C 272 PHE 0.014 0.001 PHE F 143 TRP 0.002 0.000 TRP D 256 HIS 0.006 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00372 (10434) covalent geometry : angle 0.55148 (14112) hydrogen bonds : bond 0.04010 ( 578) hydrogen bonds : angle 4.15949 ( 1698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.461 Fit side-chains REVERT: A 263 MET cc_start: 0.7573 (mtt) cc_final: 0.7164 (mtp) REVERT: B 263 MET cc_start: 0.7317 (mtt) cc_final: 0.6889 (mtp) REVERT: C 263 MET cc_start: 0.7693 (mtt) cc_final: 0.7429 (mtt) REVERT: C 280 MET cc_start: 0.6664 (tpp) cc_final: 0.6198 (tpt) REVERT: C 297 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: D 280 MET cc_start: 0.7130 (mmm) cc_final: 0.6915 (mmm) REVERT: E 222 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8370 (tpp) REVERT: E 225 GLU cc_start: 0.7333 (tp30) cc_final: 0.6440 (mm-30) REVERT: E 231 GLU cc_start: 0.7362 (tt0) cc_final: 0.6862 (tt0) REVERT: E 263 MET cc_start: 0.7513 (mtt) cc_final: 0.7223 (mtt) REVERT: F 263 MET cc_start: 0.7612 (mtt) cc_final: 0.7144 (mtp) outliers start: 24 outliers final: 9 residues processed: 96 average time/residue: 0.0808 time to fit residues: 12.4789 Evaluate side-chains 93 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 264 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 0.0370 chunk 78 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.251743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.204648 restraints weight = 89764.884| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 9.14 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10434 Z= 0.112 Angle : 0.514 11.168 14112 Z= 0.252 Chirality : 0.039 0.140 1578 Planarity : 0.003 0.033 1800 Dihedral : 3.746 15.660 1362 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.78 % Allowed : 11.76 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.24), residues: 1260 helix: 1.26 (0.18), residues: 804 sheet: -1.56 (0.55), residues: 60 loop : 0.07 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 133 TYR 0.011 0.001 TYR C 272 PHE 0.010 0.001 PHE A 143 TRP 0.002 0.000 TRP D 256 HIS 0.005 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00260 (10434) covalent geometry : angle 0.51388 (14112) hydrogen bonds : bond 0.03693 ( 578) hydrogen bonds : angle 4.07224 ( 1698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.392 Fit side-chains REVERT: A 113 MET cc_start: 0.5839 (mmm) cc_final: 0.5587 (mmm) REVERT: A 263 MET cc_start: 0.7475 (mtt) cc_final: 0.7043 (mtp) REVERT: B 263 MET cc_start: 0.7619 (mtt) cc_final: 0.7101 (mtp) REVERT: C 263 MET cc_start: 0.7629 (mtt) cc_final: 0.7360 (mtt) REVERT: C 280 MET cc_start: 0.6769 (tpp) cc_final: 0.6340 (tpt) REVERT: D 280 MET cc_start: 0.7177 (mmm) cc_final: 0.6965 (mmm) REVERT: E 225 GLU cc_start: 0.7308 (tp30) cc_final: 0.6386 (mm-30) REVERT: E 231 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: E 263 MET cc_start: 0.7625 (mtt) cc_final: 0.7350 (mtt) REVERT: F 225 GLU cc_start: 0.7364 (tp30) cc_final: 0.6557 (mm-30) REVERT: F 263 MET cc_start: 0.7549 (mtt) cc_final: 0.7118 (mtp) outliers start: 20 outliers final: 13 residues processed: 96 average time/residue: 0.0784 time to fit residues: 12.0540 Evaluate side-chains 97 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 123 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 HIS E 244 GLN F 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.246968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.200145 restraints weight = 89089.274| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 9.23 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10434 Z= 0.142 Angle : 0.540 12.034 14112 Z= 0.267 Chirality : 0.040 0.139 1578 Planarity : 0.003 0.032 1800 Dihedral : 3.740 15.976 1362 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.23 % Allowed : 11.68 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.24), residues: 1260 helix: 1.21 (0.18), residues: 804 sheet: -1.63 (0.55), residues: 60 loop : 0.02 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 305 TYR 0.012 0.001 TYR C 272 PHE 0.015 0.001 PHE C 143 TRP 0.002 0.000 TRP D 256 HIS 0.005 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00349 (10434) covalent geometry : angle 0.54047 (14112) hydrogen bonds : bond 0.03937 ( 578) hydrogen bonds : angle 4.11094 ( 1698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.394 Fit side-chains REVERT: A 113 MET cc_start: 0.6089 (mmm) cc_final: 0.5872 (mmm) REVERT: A 263 MET cc_start: 0.7586 (mtt) cc_final: 0.7173 (mtp) REVERT: B 263 MET cc_start: 0.7708 (mtt) cc_final: 0.7236 (mtp) REVERT: B 297 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: C 263 MET cc_start: 0.7710 (mtt) cc_final: 0.7452 (mtt) REVERT: C 280 MET cc_start: 0.6734 (tpp) cc_final: 0.6329 (tpt) REVERT: D 225 GLU cc_start: 0.7279 (tp30) cc_final: 0.6523 (mm-30) REVERT: D 280 MET cc_start: 0.6978 (mmm) cc_final: 0.6610 (tpp) REVERT: E 225 GLU cc_start: 0.7393 (tp30) cc_final: 0.6505 (mm-30) REVERT: E 231 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6653 (tt0) REVERT: E 263 MET cc_start: 0.7568 (mtt) cc_final: 0.7332 (mtt) REVERT: F 225 GLU cc_start: 0.7459 (tp30) cc_final: 0.6672 (mm-30) REVERT: F 263 MET cc_start: 0.7523 (mtt) cc_final: 0.7115 (mtp) outliers start: 25 outliers final: 14 residues processed: 101 average time/residue: 0.0824 time to fit residues: 13.1702 Evaluate side-chains 97 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 264 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.248614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.202044 restraints weight = 90906.842| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 9.13 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10434 Z= 0.122 Angle : 0.528 12.258 14112 Z= 0.257 Chirality : 0.039 0.140 1578 Planarity : 0.003 0.032 1800 Dihedral : 3.705 16.333 1362 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.05 % Allowed : 12.03 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.24), residues: 1260 helix: 1.30 (0.18), residues: 804 sheet: -1.63 (0.55), residues: 60 loop : 0.05 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 133 TYR 0.011 0.001 TYR C 272 PHE 0.014 0.001 PHE A 143 TRP 0.002 0.000 TRP D 256 HIS 0.005 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00291 (10434) covalent geometry : angle 0.52829 (14112) hydrogen bonds : bond 0.03740 ( 578) hydrogen bonds : angle 4.06730 ( 1698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.456 Fit side-chains REVERT: A 113 MET cc_start: 0.5973 (mmm) cc_final: 0.5622 (mmm) REVERT: A 263 MET cc_start: 0.7466 (mtt) cc_final: 0.7049 (mtp) REVERT: B 225 GLU cc_start: 0.7153 (tp30) cc_final: 0.6892 (mm-30) REVERT: B 263 MET cc_start: 0.7671 (mtt) cc_final: 0.7139 (mtp) REVERT: B 297 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: C 225 GLU cc_start: 0.7412 (tp30) cc_final: 0.6635 (mm-30) REVERT: C 258 SER cc_start: 0.8344 (m) cc_final: 0.8122 (m) REVERT: C 263 MET cc_start: 0.7456 (mtt) cc_final: 0.7237 (mtt) REVERT: C 280 MET cc_start: 0.6799 (tpp) cc_final: 0.6397 (tpt) REVERT: D 225 GLU cc_start: 0.7225 (tp30) cc_final: 0.6497 (mm-30) REVERT: E 144 MET cc_start: 0.7382 (mmm) cc_final: 0.6983 (mmm) REVERT: E 225 GLU cc_start: 0.7349 (tp30) cc_final: 0.6404 (mm-30) REVERT: E 231 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6636 (tt0) REVERT: E 263 MET cc_start: 0.7538 (mtt) cc_final: 0.7301 (mtt) REVERT: E 276 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.5938 (tt) REVERT: F 225 GLU cc_start: 0.7305 (tp30) cc_final: 0.6559 (mm-30) REVERT: F 263 MET cc_start: 0.7492 (mtt) cc_final: 0.7057 (mtp) outliers start: 23 outliers final: 16 residues processed: 102 average time/residue: 0.0793 time to fit residues: 12.9241 Evaluate side-chains 103 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 264 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.246750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.200258 restraints weight = 92187.055| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 9.13 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10434 Z= 0.133 Angle : 0.542 12.425 14112 Z= 0.264 Chirality : 0.040 0.138 1578 Planarity : 0.003 0.035 1800 Dihedral : 3.697 16.804 1362 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.78 % Allowed : 12.66 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.24), residues: 1260 helix: 1.25 (0.18), residues: 804 sheet: -1.66 (0.55), residues: 60 loop : 0.05 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 305 TYR 0.012 0.001 TYR C 272 PHE 0.013 0.001 PHE E 143 TRP 0.002 0.000 TRP D 256 HIS 0.005 0.001 HIS F 250 Details of bonding type rmsd covalent geometry : bond 0.00324 (10434) covalent geometry : angle 0.54176 (14112) hydrogen bonds : bond 0.03823 ( 578) hydrogen bonds : angle 4.09298 ( 1698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.456 Fit side-chains REVERT: A 113 MET cc_start: 0.5982 (mmm) cc_final: 0.5714 (mmm) REVERT: A 144 MET cc_start: 0.6911 (mmm) cc_final: 0.5892 (mmm) REVERT: A 225 GLU cc_start: 0.7437 (tp30) cc_final: 0.6587 (mm-30) REVERT: A 263 MET cc_start: 0.7650 (mtt) cc_final: 0.7218 (mtp) REVERT: B 225 GLU cc_start: 0.7116 (tp30) cc_final: 0.6888 (mm-30) REVERT: B 263 MET cc_start: 0.7730 (mtt) cc_final: 0.7212 (mtp) REVERT: B 297 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6381 (pm20) REVERT: C 225 GLU cc_start: 0.7425 (tp30) cc_final: 0.6569 (mm-30) REVERT: C 258 SER cc_start: 0.8413 (m) cc_final: 0.8186 (m) REVERT: C 263 MET cc_start: 0.7707 (mtt) cc_final: 0.7211 (mtp) REVERT: C 280 MET cc_start: 0.6755 (tpp) cc_final: 0.6353 (tpt) REVERT: D 225 GLU cc_start: 0.7322 (tp30) cc_final: 0.6535 (mm-30) REVERT: E 144 MET cc_start: 0.7333 (mmm) cc_final: 0.6971 (mmm) REVERT: E 231 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: E 263 MET cc_start: 0.7562 (mtt) cc_final: 0.7336 (mtt) REVERT: F 225 GLU cc_start: 0.7319 (tp30) cc_final: 0.6481 (mm-30) REVERT: F 263 MET cc_start: 0.7612 (mtt) cc_final: 0.7192 (mtp) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.0791 time to fit residues: 12.9955 Evaluate side-chains 102 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 102 optimal weight: 0.0870 chunk 123 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 GLN F 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.250529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.205315 restraints weight = 89636.596| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 8.17 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10434 Z= 0.107 Angle : 0.535 12.997 14112 Z= 0.255 Chirality : 0.039 0.138 1578 Planarity : 0.003 0.035 1800 Dihedral : 3.633 16.626 1362 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.78 % Allowed : 12.66 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.24), residues: 1260 helix: 1.40 (0.18), residues: 804 sheet: -1.63 (0.56), residues: 60 loop : 0.15 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 183 TYR 0.010 0.001 TYR C 272 PHE 0.010 0.001 PHE F 143 TRP 0.002 0.000 TRP D 256 HIS 0.005 0.001 HIS F 250 Details of bonding type rmsd covalent geometry : bond 0.00246 (10434) covalent geometry : angle 0.53454 (14112) hydrogen bonds : bond 0.03608 ( 578) hydrogen bonds : angle 4.03801 ( 1698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.267 Fit side-chains REVERT: A 113 MET cc_start: 0.6028 (mmm) cc_final: 0.5740 (mmm) REVERT: A 144 MET cc_start: 0.6869 (mmm) cc_final: 0.5847 (mmm) REVERT: A 225 GLU cc_start: 0.7195 (tp30) cc_final: 0.6365 (mm-30) REVERT: A 263 MET cc_start: 0.7451 (mtt) cc_final: 0.7048 (mtp) REVERT: B 225 GLU cc_start: 0.7105 (tp30) cc_final: 0.6873 (mm-30) REVERT: B 263 MET cc_start: 0.7870 (mtt) cc_final: 0.7289 (mtp) REVERT: B 297 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6513 (pm20) REVERT: C 225 GLU cc_start: 0.7408 (tp30) cc_final: 0.6642 (mm-30) REVERT: C 258 SER cc_start: 0.8228 (m) cc_final: 0.8011 (m) REVERT: C 263 MET cc_start: 0.7555 (mtt) cc_final: 0.7335 (mtt) REVERT: C 280 MET cc_start: 0.7115 (tpp) cc_final: 0.6635 (tpt) REVERT: D 225 GLU cc_start: 0.7135 (tp30) cc_final: 0.6401 (mm-30) REVERT: D 280 MET cc_start: 0.7139 (mmm) cc_final: 0.6409 (tpt) REVERT: E 144 MET cc_start: 0.7296 (mmm) cc_final: 0.6879 (mmm) REVERT: E 225 GLU cc_start: 0.7633 (tp30) cc_final: 0.6634 (mm-30) REVERT: E 231 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: E 263 MET cc_start: 0.7708 (mtt) cc_final: 0.7442 (mtt) REVERT: F 225 GLU cc_start: 0.7090 (tp30) cc_final: 0.6214 (mm-30) REVERT: F 263 MET cc_start: 0.7658 (mtt) cc_final: 0.7207 (mtp) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.0795 time to fit residues: 12.7983 Evaluate side-chains 105 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 15 optimal weight: 0.0070 chunk 42 optimal weight: 10.0000 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 GLN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.248665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.202923 restraints weight = 88828.500| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 8.54 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10434 Z= 0.122 Angle : 0.542 12.628 14112 Z= 0.260 Chirality : 0.039 0.140 1578 Planarity : 0.003 0.035 1800 Dihedral : 3.627 16.738 1362 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.69 % Allowed : 12.66 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.24), residues: 1260 helix: 1.37 (0.18), residues: 804 sheet: -1.65 (0.56), residues: 60 loop : 0.12 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 133 TYR 0.010 0.001 TYR A 272 PHE 0.011 0.001 PHE E 143 TRP 0.001 0.000 TRP D 256 HIS 0.005 0.001 HIS F 250 Details of bonding type rmsd covalent geometry : bond 0.00294 (10434) covalent geometry : angle 0.54168 (14112) hydrogen bonds : bond 0.03713 ( 578) hydrogen bonds : angle 4.04346 ( 1698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.71 seconds wall clock time: 29 minutes 43.11 seconds (1783.11 seconds total)