Starting phenix.real_space_refine on Tue Feb 3 20:36:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e02_47346/02_2026/9e02_47346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e02_47346/02_2026/9e02_47346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e02_47346/02_2026/9e02_47346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e02_47346/02_2026/9e02_47346.map" model { file = "/net/cci-nas-00/data/ceres_data/9e02_47346/02_2026/9e02_47346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e02_47346/02_2026/9e02_47346.cif" } resolution = 2.5 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= 0.016 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4599 2.51 5 N 1005 2.21 5 O 1071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6708 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "F" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 341 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "A" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 341 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "C" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 341 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Time building chain proxies: 1.21, per 1000 atoms: 0.18 Number of scatterers: 6708 At special positions: 0 Unit cell: (98.328, 96.882, 87.483, 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 33 16.00 O 1071 8.00 N 1005 7.00 C 4599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 186.8 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 91.2% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'E' and resid 4 through 33 removed outlier: 4.298A pdb=" N HIS E 8 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 12 " --> pdb=" O HIS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 61 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 163 through 196 removed outlier: 3.557A pdb=" N ALA E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) Proline residue: E 185 - end of helix Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 200 through 228 removed outlier: 3.607A pdb=" N LYS E 205 " --> pdb=" O ASP E 201 " (cutoff:3.500A) Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 228 through 241 removed outlier: 3.964A pdb=" N PHE E 232 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 282 removed outlier: 3.955A pdb=" N GLY E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Proline residue: E 272 - end of helix Processing helix chain 'E' and resid 285 through 292 Processing helix chain 'E' and resid 292 through 307 removed outlier: 3.832A pdb=" N VAL E 298 " --> pdb=" O LYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 336 Proline residue: E 321 - end of helix Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 24 through 44 Processing helix chain 'A' and resid 5 through 33 removed outlier: 3.769A pdb=" N LEU A 12 " --> pdb=" O HIS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 61 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 163 through 196 removed outlier: 3.519A pdb=" N ALA A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 200 through 228 removed outlier: 3.560A pdb=" N LYS A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.930A pdb=" N PHE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 282 removed outlier: 3.925A pdb=" N GLY A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 292 through 308 removed outlier: 3.813A pdb=" N VAL A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 336 Proline residue: A 321 - end of helix Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 24 through 44 Processing helix chain 'C' and resid 5 through 33 removed outlier: 3.700A pdb=" N LEU C 12 " --> pdb=" O HIS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 61 Proline residue: C 44 - end of helix Processing helix chain 'C' and resid 163 through 196 removed outlier: 3.558A pdb=" N ALA C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) Proline residue: C 185 - end of helix Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 200 through 228 removed outlier: 3.727A pdb=" N LYS C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.938A pdb=" N PHE C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 282 removed outlier: 3.840A pdb=" N GLY C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 292 through 307 removed outlier: 3.782A pdb=" N VAL C 298 " --> pdb=" O LYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 336 Proline residue: C 321 - end of helix Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 24 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 6.092A pdb=" N THR E 246 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N THR A 246 " --> pdb=" O THR C 161 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.72 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: 1884 1.34 - 1.46: 1152 1.46 - 1.57: 3786 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6888 Sorted by residual: bond pdb=" C LEU C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.10e+00 bond pdb=" C LEU A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.98e+00 bond pdb=" C LEU E 208 " pdb=" N PRO E 209 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.62e+00 bond pdb=" C ALA C 196 " pdb=" N PRO C 197 " ideal model delta sigma weight residual 1.337 1.352 -0.015 9.80e-03 1.04e+04 2.48e+00 bond pdb=" C ALA A 196 " pdb=" N PRO A 197 " ideal model delta sigma weight residual 1.337 1.351 -0.015 9.80e-03 1.04e+04 2.27e+00 ... (remaining 6883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 9070 1.58 - 3.16: 235 3.16 - 4.75: 23 4.75 - 6.33: 26 6.33 - 7.91: 3 Bond angle restraints: 9357 Sorted by residual: angle pdb=" N GLY A 165 " pdb=" CA GLY A 165 " pdb=" C GLY A 165 " ideal model delta sigma weight residual 113.27 108.57 4.70 1.33e+00 5.65e-01 1.25e+01 angle pdb=" N GLY C 165 " pdb=" CA GLY C 165 " pdb=" C GLY C 165 " ideal model delta sigma weight residual 113.27 108.94 4.33 1.33e+00 5.65e-01 1.06e+01 angle pdb=" CB LYS C 205 " pdb=" CG LYS C 205 " pdb=" CD LYS C 205 " ideal model delta sigma weight residual 111.30 118.35 -7.05 2.30e+00 1.89e-01 9.39e+00 angle pdb=" N TYR A 227 " pdb=" CA TYR A 227 " pdb=" C TYR A 227 " ideal model delta sigma weight residual 111.36 114.59 -3.23 1.09e+00 8.42e-01 8.76e+00 angle pdb=" N TYR E 227 " pdb=" CA TYR E 227 " pdb=" C TYR E 227 " ideal model delta sigma weight residual 111.36 114.44 -3.08 1.09e+00 8.42e-01 7.99e+00 ... (remaining 9352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3337 16.92 - 33.85: 453 33.85 - 50.77: 143 50.77 - 67.69: 23 67.69 - 84.61: 7 Dihedral angle restraints: 3963 sinusoidal: 1521 harmonic: 2442 Sorted by residual: dihedral pdb=" CA VAL A 164 " pdb=" C VAL A 164 " pdb=" N GLY A 165 " pdb=" CA GLY A 165 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CB GLU A 203 " pdb=" CG GLU A 203 " pdb=" CD GLU A 203 " pdb=" OE1 GLU A 203 " ideal model delta sinusoidal sigma weight residual 0.00 -84.61 84.61 1 3.00e+01 1.11e-03 9.67e+00 dihedral pdb=" CB GLU E 203 " pdb=" CG GLU E 203 " pdb=" CD GLU E 203 " pdb=" OE1 GLU E 203 " ideal model delta sinusoidal sigma weight residual 0.00 -83.98 83.98 1 3.00e+01 1.11e-03 9.55e+00 ... (remaining 3960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 673 0.032 - 0.063: 300 0.063 - 0.095: 121 0.095 - 0.127: 22 0.127 - 0.158: 6 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA VAL E 164 " pdb=" N VAL E 164 " pdb=" C VAL E 164 " pdb=" CB VAL E 164 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CB ILE C 238 " pdb=" CA ILE C 238 " pdb=" CG1 ILE C 238 " pdb=" CG2 ILE C 238 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA THR E 230 " pdb=" N THR E 230 " pdb=" C THR E 230 " pdb=" CB THR E 230 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 1119 not shown) Planarity restraints: 1119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 226 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C TYR E 226 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR E 226 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 227 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 226 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C TYR C 226 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR C 226 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR C 227 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 226 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C TYR A 226 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR A 226 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR A 227 " 0.021 2.00e-02 2.50e+03 ... (remaining 1116 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 202 2.71 - 3.26: 6941 3.26 - 3.81: 11596 3.81 - 4.35: 13216 4.35 - 4.90: 23093 Nonbonded interactions: 55048 Sorted by model distance: nonbonded pdb=" O ALA E 304 " pdb=" OG1 THR E 308 " model vdw 2.166 3.040 nonbonded pdb=" O ALA C 304 " pdb=" OG1 THR C 308 " model vdw 2.172 3.040 nonbonded pdb=" O ALA A 304 " pdb=" OG1 THR A 308 " model vdw 2.184 3.040 nonbonded pdb=" O LEU C 38 " pdb=" OG1 THR C 42 " model vdw 2.243 3.040 nonbonded pdb=" O LEU A 38 " pdb=" OG1 THR A 42 " model vdw 2.256 3.040 ... (remaining 55043 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' 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: 3.390 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.045 6888 Z= 0.212 Angle : 0.646 7.911 9357 Z= 0.367 Chirality : 0.041 0.158 1122 Planarity : 0.006 0.076 1119 Dihedral : 17.346 84.613 2391 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.80 % Allowed : 26.75 % Favored : 70.45 % 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 are not related in a simple way. whole: 2.27 (0.29), residues: 831 helix: 2.38 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -3.89 (0.41), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 13 TYR 0.015 0.001 TYR A 276 PHE 0.019 0.002 PHE A 258 TRP 0.025 0.003 TRP A 189 HIS 0.008 0.002 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 6888) covalent geometry : angle 0.64584 ( 9357) hydrogen bonds : bond 0.09191 ( 575) hydrogen bonds : angle 4.99811 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.240 Fit side-chains REVERT: F 29 MET cc_start: 0.6777 (tmm) cc_final: 0.6293 (tmm) REVERT: A 43 LYS cc_start: 0.8295 (tppp) cc_final: 0.8083 (tppp) REVERT: A 57 GLU cc_start: 0.7576 (tp30) cc_final: 0.7348 (mp0) REVERT: A 318 MET cc_start: 0.8470 (tpp) cc_final: 0.7885 (tpp) REVERT: B 29 MET cc_start: 0.6633 (tmm) cc_final: 0.6371 (tmm) REVERT: C 274 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7478 (t) REVERT: C 318 MET cc_start: 0.8393 (tpp) cc_final: 0.7885 (tpp) REVERT: D 29 MET cc_start: 0.6966 (tmm) cc_final: 0.6643 (tmm) outliers start: 20 outliers final: 17 residues processed: 144 average time/residue: 0.2503 time to fit residues: 39.4696 Evaluate side-chains 144 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS A 47 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118593 restraints weight = 8211.113| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.59 r_work: 0.3419 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6888 Z= 0.147 Angle : 0.547 7.292 9357 Z= 0.279 Chirality : 0.040 0.176 1122 Planarity : 0.005 0.066 1119 Dihedral : 7.427 58.177 911 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.90 % Allowed : 21.99 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.29), residues: 831 helix: 2.42 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -3.87 (0.47), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.014 0.001 TYR A 227 PHE 0.021 0.001 PHE E 169 TRP 0.019 0.002 TRP A 189 HIS 0.008 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6888) covalent geometry : angle 0.54705 ( 9357) hydrogen bonds : bond 0.04487 ( 575) hydrogen bonds : angle 4.21878 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.146 Fit side-chains REVERT: F 29 MET cc_start: 0.6768 (tmm) cc_final: 0.6279 (tmm) REVERT: A 43 LYS cc_start: 0.8395 (tppp) cc_final: 0.8192 (tppp) REVERT: A 61 MET cc_start: 0.5613 (tmm) cc_final: 0.5295 (tmm) REVERT: A 250 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7940 (p0) REVERT: A 260 LYS cc_start: 0.8455 (mmtm) cc_final: 0.7962 (mmtm) REVERT: A 318 MET cc_start: 0.8484 (tpp) cc_final: 0.7833 (tpp) REVERT: B 29 MET cc_start: 0.6563 (tmm) cc_final: 0.6304 (tmm) REVERT: C 158 MET cc_start: 0.5963 (tpp) cc_final: 0.3767 (pmt) REVERT: C 318 MET cc_start: 0.8390 (tpp) cc_final: 0.7840 (tpp) REVERT: D 29 MET cc_start: 0.6913 (tmm) cc_final: 0.6590 (tmm) outliers start: 35 outliers final: 17 residues processed: 158 average time/residue: 0.2567 time to fit residues: 44.2543 Evaluate side-chains 149 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 36 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: ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116508 restraints weight = 8085.984| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.55 r_work: 0.3385 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6888 Z= 0.219 Angle : 0.606 7.861 9357 Z= 0.309 Chirality : 0.043 0.174 1122 Planarity : 0.005 0.065 1119 Dihedral : 6.975 58.343 896 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.90 % Allowed : 20.31 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.29), residues: 831 helix: 2.41 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -3.97 (0.40), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.015 0.001 TYR C 227 PHE 0.022 0.002 PHE E 169 TRP 0.026 0.003 TRP C 189 HIS 0.009 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 6888) covalent geometry : angle 0.60609 ( 9357) hydrogen bonds : bond 0.05197 ( 575) hydrogen bonds : angle 4.31124 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.262 Fit side-chains REVERT: E 203 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6764 (mm-30) REVERT: F 29 MET cc_start: 0.6769 (tmm) cc_final: 0.6289 (tmm) REVERT: A 43 LYS cc_start: 0.8414 (tppp) cc_final: 0.8208 (tppp) REVERT: A 57 GLU cc_start: 0.7579 (tp30) cc_final: 0.7295 (mp0) REVERT: A 61 MET cc_start: 0.5739 (tmm) cc_final: 0.5466 (tmm) REVERT: A 318 MET cc_start: 0.8502 (tpp) cc_final: 0.7859 (tpp) REVERT: B 29 MET cc_start: 0.6575 (tmm) cc_final: 0.6302 (tmm) REVERT: C 163 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: C 274 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7556 (t) REVERT: C 318 MET cc_start: 0.8401 (tpp) cc_final: 0.7824 (tpp) REVERT: D 29 MET cc_start: 0.6931 (tmm) cc_final: 0.6617 (tmm) outliers start: 35 outliers final: 20 residues processed: 159 average time/residue: 0.2692 time to fit residues: 46.6531 Evaluate side-chains 152 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 34 optimal weight: 0.5980 chunk 77 optimal weight: 0.0970 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS A 47 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118508 restraints weight = 8176.356| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.58 r_work: 0.3419 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6888 Z= 0.140 Angle : 0.531 8.042 9357 Z= 0.270 Chirality : 0.039 0.134 1122 Planarity : 0.005 0.060 1119 Dihedral : 6.580 58.844 894 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.34 % Allowed : 20.03 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.29), residues: 831 helix: 2.51 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -3.60 (0.47), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.009 0.001 TYR A 276 PHE 0.020 0.001 PHE E 169 TRP 0.018 0.002 TRP C 189 HIS 0.008 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6888) covalent geometry : angle 0.53130 ( 9357) hydrogen bonds : bond 0.04309 ( 575) hydrogen bonds : angle 4.12355 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.287 Fit side-chains REVERT: E 158 MET cc_start: 0.6259 (tpp) cc_final: 0.3865 (pmt) REVERT: F 29 MET cc_start: 0.6761 (tmm) cc_final: 0.6273 (tmm) REVERT: A 61 MET cc_start: 0.5608 (tmm) cc_final: 0.5377 (tmm) REVERT: A 250 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7904 (p0) REVERT: A 318 MET cc_start: 0.8472 (tpp) cc_final: 0.7866 (tpp) REVERT: B 29 MET cc_start: 0.6545 (tmm) cc_final: 0.6286 (tmm) REVERT: C 158 MET cc_start: 0.6013 (tpp) cc_final: 0.3845 (pmt) REVERT: C 289 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (mt) REVERT: D 29 MET cc_start: 0.6903 (tmm) cc_final: 0.6588 (tmm) outliers start: 31 outliers final: 19 residues processed: 150 average time/residue: 0.2815 time to fit residues: 46.0510 Evaluate side-chains 149 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 8 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: ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN A 47 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116447 restraints weight = 8183.278| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.58 r_work: 0.3384 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6888 Z= 0.210 Angle : 0.594 8.616 9357 Z= 0.304 Chirality : 0.043 0.136 1122 Planarity : 0.005 0.061 1119 Dihedral : 6.584 59.020 891 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.06 % Allowed : 20.73 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.29), residues: 831 helix: 2.44 (0.19), residues: 714 sheet: None (None), residues: 0 loop : -3.53 (0.45), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.011 0.001 TYR C 227 PHE 0.021 0.002 PHE E 169 TRP 0.022 0.002 TRP A 189 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 6888) covalent geometry : angle 0.59373 ( 9357) hydrogen bonds : bond 0.05070 ( 575) hydrogen bonds : angle 4.28527 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.151 Fit side-chains REVERT: F 29 MET cc_start: 0.6786 (tmm) cc_final: 0.6299 (tmm) REVERT: A 57 GLU cc_start: 0.7576 (tp30) cc_final: 0.7292 (mp0) REVERT: A 318 MET cc_start: 0.8507 (tpp) cc_final: 0.7870 (tpp) REVERT: B 29 MET cc_start: 0.6591 (tmm) cc_final: 0.6324 (tmm) REVERT: C 158 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.3821 (pmt) REVERT: D 29 MET cc_start: 0.6976 (tmm) cc_final: 0.6661 (tmm) outliers start: 29 outliers final: 22 residues processed: 149 average time/residue: 0.2656 time to fit residues: 43.3138 Evaluate side-chains 149 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS A 47 ASN A 162 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117096 restraints weight = 8171.609| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.58 r_work: 0.3395 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6888 Z= 0.176 Angle : 0.568 7.501 9357 Z= 0.290 Chirality : 0.041 0.133 1122 Planarity : 0.005 0.060 1119 Dihedral : 6.511 59.141 891 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.90 % Allowed : 19.61 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.29), residues: 831 helix: 2.40 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -3.35 (0.50), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.009 0.001 TYR E 254 PHE 0.019 0.001 PHE E 169 TRP 0.019 0.002 TRP A 189 HIS 0.011 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6888) covalent geometry : angle 0.56850 ( 9357) hydrogen bonds : bond 0.04748 ( 575) hydrogen bonds : angle 4.23234 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.153 Fit side-chains REVERT: E 158 MET cc_start: 0.6366 (tpp) cc_final: 0.3881 (pmt) REVERT: F 29 MET cc_start: 0.6777 (tmm) cc_final: 0.6290 (tmm) REVERT: A 57 GLU cc_start: 0.7574 (tp30) cc_final: 0.7302 (mp0) REVERT: A 287 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6576 (mttp) REVERT: A 318 MET cc_start: 0.8495 (tpp) cc_final: 0.7861 (tpp) REVERT: B 29 MET cc_start: 0.6547 (tmm) cc_final: 0.6277 (tmm) REVERT: C 61 MET cc_start: 0.5452 (tmm) cc_final: 0.5032 (tmm) REVERT: C 158 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.3843 (pmt) REVERT: D 29 MET cc_start: 0.6921 (tmm) cc_final: 0.6609 (tmm) outliers start: 35 outliers final: 21 residues processed: 150 average time/residue: 0.2800 time to fit residues: 45.8160 Evaluate side-chains 147 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS A 47 ASN A 162 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117639 restraints weight = 8100.877| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.57 r_work: 0.3403 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6888 Z= 0.162 Angle : 0.577 8.882 9357 Z= 0.288 Chirality : 0.041 0.162 1122 Planarity : 0.005 0.059 1119 Dihedral : 6.438 59.988 891 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.48 % Allowed : 20.45 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.29), residues: 831 helix: 2.46 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -3.27 (0.51), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.008 0.001 TYR E 254 PHE 0.017 0.001 PHE E 169 TRP 0.017 0.002 TRP A 189 HIS 0.006 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6888) covalent geometry : angle 0.57703 ( 9357) hydrogen bonds : bond 0.04595 ( 575) hydrogen bonds : angle 4.19053 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.247 Fit side-chains REVERT: E 158 MET cc_start: 0.6334 (tpp) cc_final: 0.3895 (pmt) REVERT: F 29 MET cc_start: 0.6766 (tmm) cc_final: 0.6279 (tmm) REVERT: A 57 GLU cc_start: 0.7589 (tp30) cc_final: 0.7305 (mp0) REVERT: A 250 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8032 (p0) REVERT: A 287 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6576 (mttt) REVERT: A 318 MET cc_start: 0.8473 (tpp) cc_final: 0.7842 (tpp) REVERT: B 29 MET cc_start: 0.6542 (tmm) cc_final: 0.6269 (tmm) REVERT: C 61 MET cc_start: 0.5424 (tmm) cc_final: 0.4993 (tmm) REVERT: C 158 MET cc_start: 0.6053 (tpp) cc_final: 0.3859 (pmt) REVERT: D 29 MET cc_start: 0.6913 (tmm) cc_final: 0.6601 (tmm) outliers start: 32 outliers final: 21 residues processed: 147 average time/residue: 0.2873 time to fit residues: 46.2560 Evaluate side-chains 149 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS A 47 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117430 restraints weight = 8185.063| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.59 r_work: 0.3400 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6888 Z= 0.165 Angle : 0.569 7.710 9357 Z= 0.288 Chirality : 0.041 0.136 1122 Planarity : 0.005 0.058 1119 Dihedral : 6.410 59.531 891 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.34 % Allowed : 20.87 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.29), residues: 831 helix: 2.43 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -3.28 (0.49), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.008 0.001 TYR E 254 PHE 0.021 0.001 PHE E 169 TRP 0.017 0.002 TRP A 189 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6888) covalent geometry : angle 0.56944 ( 9357) hydrogen bonds : bond 0.04625 ( 575) hydrogen bonds : angle 4.19644 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.256 Fit side-chains REVERT: E 158 MET cc_start: 0.6338 (tpp) cc_final: 0.3890 (pmt) REVERT: F 29 MET cc_start: 0.6748 (tmm) cc_final: 0.6266 (tmm) REVERT: A 57 GLU cc_start: 0.7569 (tp30) cc_final: 0.7286 (mp0) REVERT: A 162 HIS cc_start: 0.8081 (p-80) cc_final: 0.7852 (p-80) REVERT: A 250 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8037 (p0) REVERT: A 287 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6579 (mttp) REVERT: A 318 MET cc_start: 0.8471 (tpp) cc_final: 0.7840 (tpp) REVERT: B 29 MET cc_start: 0.6539 (tmm) cc_final: 0.6264 (tmm) REVERT: C 61 MET cc_start: 0.5459 (tmm) cc_final: 0.5029 (tmm) REVERT: C 158 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.3851 (pmt) REVERT: D 29 MET cc_start: 0.6911 (tmm) cc_final: 0.6598 (tmm) outliers start: 31 outliers final: 22 residues processed: 148 average time/residue: 0.3063 time to fit residues: 49.3654 Evaluate side-chains 151 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS A 47 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117661 restraints weight = 8265.181| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.60 r_work: 0.3409 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6888 Z= 0.155 Angle : 0.570 9.147 9357 Z= 0.286 Chirality : 0.040 0.130 1122 Planarity : 0.005 0.057 1119 Dihedral : 6.376 59.535 890 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.92 % Allowed : 21.01 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.29), residues: 831 helix: 2.52 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -3.23 (0.51), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.008 0.001 TYR E 254 PHE 0.023 0.001 PHE E 169 TRP 0.015 0.002 TRP A 189 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6888) covalent geometry : angle 0.57013 ( 9357) hydrogen bonds : bond 0.04507 ( 575) hydrogen bonds : angle 4.15090 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.194 Fit side-chains REVERT: E 158 MET cc_start: 0.6314 (tpp) cc_final: 0.3922 (pmt) REVERT: F 29 MET cc_start: 0.6792 (tmm) cc_final: 0.6307 (tmm) REVERT: A 57 GLU cc_start: 0.7617 (tp30) cc_final: 0.7336 (mp0) REVERT: A 250 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7998 (p0) REVERT: A 287 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6579 (mttt) REVERT: A 318 MET cc_start: 0.8448 (tpp) cc_final: 0.7811 (tpp) REVERT: B 29 MET cc_start: 0.6573 (tmm) cc_final: 0.6302 (tmm) REVERT: C 61 MET cc_start: 0.5438 (tmm) cc_final: 0.5009 (tmm) REVERT: C 158 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.3812 (pmt) REVERT: D 29 MET cc_start: 0.6931 (tmm) cc_final: 0.6621 (tmm) outliers start: 28 outliers final: 21 residues processed: 144 average time/residue: 0.2528 time to fit residues: 39.9759 Evaluate side-chains 148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS E 250 ASN A 47 ASN A 162 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116111 restraints weight = 8175.836| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.60 r_work: 0.3386 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6888 Z= 0.211 Angle : 0.605 10.620 9357 Z= 0.306 Chirality : 0.043 0.137 1122 Planarity : 0.005 0.058 1119 Dihedral : 6.450 59.657 890 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.92 % Allowed : 20.87 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.29), residues: 831 helix: 2.41 (0.19), residues: 711 sheet: None (None), residues: 0 loop : -3.44 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.008 0.001 TYR A 226 PHE 0.025 0.002 PHE E 169 TRP 0.019 0.002 TRP A 189 HIS 0.007 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 6888) covalent geometry : angle 0.60518 ( 9357) hydrogen bonds : bond 0.05032 ( 575) hydrogen bonds : angle 4.26934 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.151 Fit side-chains REVERT: E 158 MET cc_start: 0.6387 (tpp) cc_final: 0.3860 (pmt) REVERT: F 29 MET cc_start: 0.6762 (tmm) cc_final: 0.6277 (tmm) REVERT: A 57 GLU cc_start: 0.7607 (tp30) cc_final: 0.7324 (mp0) REVERT: A 287 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6620 (mttp) REVERT: A 318 MET cc_start: 0.8494 (tpp) cc_final: 0.7853 (tpp) REVERT: B 29 MET cc_start: 0.6590 (tmm) cc_final: 0.6332 (tmm) REVERT: C 61 MET cc_start: 0.5456 (tmm) cc_final: 0.5036 (tmm) REVERT: C 158 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.3829 (pmt) REVERT: D 29 MET cc_start: 0.6940 (tmm) cc_final: 0.6630 (tmm) outliers start: 28 outliers final: 22 residues processed: 146 average time/residue: 0.2455 time to fit residues: 39.2143 Evaluate side-chains 151 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 HIS A 47 ASN A 162 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116859 restraints weight = 8209.195| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.58 r_work: 0.3398 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6888 Z= 0.178 Angle : 0.594 10.435 9357 Z= 0.298 Chirality : 0.041 0.133 1122 Planarity : 0.005 0.058 1119 Dihedral : 6.405 59.486 890 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.64 % Allowed : 21.01 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.29), residues: 831 helix: 2.45 (0.19), residues: 711 sheet: None (None), residues: 0 loop : -3.44 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.008 0.001 TYR E 254 PHE 0.023 0.001 PHE E 169 TRP 0.017 0.002 TRP A 189 HIS 0.007 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 6888) covalent geometry : angle 0.59377 ( 9357) hydrogen bonds : bond 0.04774 ( 575) hydrogen bonds : angle 4.24093 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.64 seconds wall clock time: 43 minutes 40.17 seconds (2620.17 seconds total)