Starting phenix.real_space_refine on Wed Jul 1 21:09:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv6_32139/07_2026/7vv6_32139.map" } resolution = 3.3 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= 0.000 sd= 0.003 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 18 5.16 5 C 1518 2.51 5 N 342 2.21 5 O 349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2227 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2161 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.82, per 1000 atoms: 0.37 Number of scatterers: 2227 At special positions: 0 Unit cell: (65.224, 72.588, 61.016, 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 18 16.00 O 349 8.00 N 342 7.00 C 1518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 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: 0.23 Conformation dependent library (CDL) restraints added in 100.5 milliseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.529A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.831A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.602A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.339A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' 169 hydrogen bonds defined for protein. 507 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: 0.34 Time building geometry restraints manager: 0.29 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: 617 1.34 - 1.47: 662 1.47 - 1.59: 993 1.59 - 1.71: 1 1.71 - 1.84: 22 Bond restraints: 2295 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.447 1.496 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C32 6IB R 402 " pdb=" N6 6IB R 402 " ideal model delta sigma weight residual 1.449 1.497 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CB VAL R 131 " pdb=" CG2 VAL R 131 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 ... (remaining 2290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 3010 3.21 - 6.43: 103 6.43 - 9.64: 14 9.64 - 12.86: 2 12.86 - 16.07: 2 Bond angle restraints: 3131 Sorted by residual: angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 angle pdb=" C GLY R 236 " pdb=" N LEU R 237 " pdb=" CA LEU R 237 " ideal model delta sigma weight residual 120.58 127.01 -6.43 1.32e+00 5.74e-01 2.37e+01 angle pdb=" CA LEU R 226 " pdb=" CB LEU R 226 " pdb=" CG LEU R 226 " ideal model delta sigma weight residual 116.30 132.37 -16.07 3.50e+00 8.16e-02 2.11e+01 angle pdb=" N SER R 177 " pdb=" CA SER R 177 " pdb=" C SER R 177 " ideal model delta sigma weight residual 111.28 115.95 -4.67 1.09e+00 8.42e-01 1.83e+01 ... (remaining 3126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.72: 992 12.72 - 25.44: 161 25.44 - 38.16: 97 38.16 - 50.88: 32 50.88 - 63.60: 17 Dihedral angle restraints: 1299 sinusoidal: 515 harmonic: 784 Sorted by residual: dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP R 252 " pdb=" C ASP R 252 " pdb=" N SER R 253 " pdb=" CA SER R 253 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 253 0.061 - 0.122: 88 0.122 - 0.183: 23 0.183 - 0.244: 2 0.244 - 0.305: 2 Chirality restraints: 368 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 365 not shown) Planarity restraints: 361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 43 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL R 43 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL R 43 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY R 44 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 40 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ILE R 40 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 40 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA R 41 " -0.013 2.00e-02 2.50e+03 ... (remaining 358 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 629 2.81 - 3.33: 1941 3.33 - 3.86: 3854 3.86 - 4.38: 4171 4.38 - 4.90: 7427 Nonbonded interactions: 18022 Sorted by model distance: nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 3.040 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.320 3.040 nonbonded pdb=" O SER R 98 " pdb=" OG SER R 98 " model vdw 2.322 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.322 3.040 ... (remaining 18017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.410 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.410 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.010 0.134 2297 Z= 0.435 Angle : 1.380 16.073 3135 Z= 0.708 Chirality : 0.068 0.305 368 Planarity : 0.009 0.048 361 Dihedral : 19.043 63.599 785 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 10.37 % Allowed : 24.90 % Favored : 64.73 % 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: -4.22 (0.34), residues: 269 helix: -2.49 (0.23), residues: 208 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 138 TYR 0.021 0.004 TYR R 89 PHE 0.020 0.003 PHE R 183 TRP 0.015 0.003 TRP R 289 HIS 0.004 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00979 / 0.43 ( 2295) covalent geometry : angle 1.37952 / 0.71 ( 3131) SS BOND : bond 0.00539 / 0.27 ( 2) SS BOND : angle 1.88847 / 1.09 ( 4) hydrogen bonds : bond 0.11723 / 7.30 ( 169) hydrogen bonds : angle 6.91330 / 4.83 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.8309 (ttp) cc_final: 0.7998 (ttm) REVERT: R 164 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7868 (tm-30) REVERT: R 166 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8433 (tptt) REVERT: R 201 SER cc_start: 0.9194 (m) cc_final: 0.8684 (p) REVERT: R 242 GLN cc_start: 0.8817 (pp30) cc_final: 0.8517 (pp30) outliers start: 25 outliers final: 1 residues processed: 67 average time/residue: 0.0563 time to fit residues: 4.5402 Evaluate side-chains 31 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 144 HIS R 271 ASN R 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.082380 restraints weight = 3717.034| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.37 r_work: 0.2829 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2297 Z= 0.127 Angle : 0.641 9.002 3135 Z= 0.309 Chirality : 0.042 0.239 368 Planarity : 0.005 0.033 361 Dihedral : 10.016 57.185 324 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 27.80 % Favored : 69.29 % 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: 0.06 (0.49), residues: 269 helix: 0.57 (0.33), residues: 218 sheet: None (None), residues: 0 loop : -2.00 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 143 TYR 0.012 0.001 TYR R 222 PHE 0.012 0.001 PHE R 81 TRP 0.012 0.001 TRP R 248 HIS 0.002 0.001 HIS R 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 2295) covalent geometry : angle 0.64122 / 0.31 ( 3131) SS BOND : bond 0.00209 / 0.11 ( 2) SS BOND : angle 0.76622 / 0.50 ( 4) hydrogen bonds : bond 0.04195 / 2.73 ( 169) hydrogen bonds : angle 4.39978 / 3.05 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.8895 (ttp) cc_final: 0.8614 (ttm) REVERT: R 126 GLU cc_start: 0.8991 (tp30) cc_final: 0.8616 (mm-30) REVERT: R 143 ARG cc_start: 0.8421 (ptm-80) cc_final: 0.8196 (ptm-80) REVERT: R 163 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8456 (tt) REVERT: R 166 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8257 (tptt) outliers start: 7 outliers final: 2 residues processed: 39 average time/residue: 0.0574 time to fit residues: 2.7422 Evaluate side-chains 33 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 144 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.080443 restraints weight = 3957.230| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.24 r_work: 0.2813 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2297 Z= 0.134 Angle : 0.581 6.895 3135 Z= 0.281 Chirality : 0.042 0.221 368 Planarity : 0.004 0.031 361 Dihedral : 9.056 57.012 323 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.49 % Allowed : 26.97 % Favored : 70.54 % 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: 1.51 (0.52), residues: 269 helix: 1.61 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -2.04 (0.81), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 143 TYR 0.009 0.001 TYR R 222 PHE 0.008 0.001 PHE R 244 TRP 0.009 0.001 TRP R 243 HIS 0.001 0.000 HIS R 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 2295) covalent geometry : angle 0.58154 / 0.28 ( 3131) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 0.49026 / 0.36 ( 4) hydrogen bonds : bond 0.04099 / 2.65 ( 169) hydrogen bonds : angle 4.04998 / 2.80 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.085 Fit side-chains REVERT: R 109 MET cc_start: 0.8847 (ttp) cc_final: 0.8576 (ttm) REVERT: R 166 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8376 (tptt) REVERT: R 201 SER cc_start: 0.9336 (m) cc_final: 0.8930 (p) REVERT: R 242 GLN cc_start: 0.9171 (pp30) cc_final: 0.8932 (pp30) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.0664 time to fit residues: 3.0037 Evaluate side-chains 36 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 100 ASN R 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.082553 restraints weight = 3888.136| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.20 r_work: 0.2844 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2297 Z= 0.126 Angle : 0.555 6.903 3135 Z= 0.272 Chirality : 0.041 0.215 368 Planarity : 0.003 0.029 361 Dihedral : 8.888 55.718 323 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.73 % Allowed : 26.14 % Favored : 70.12 % 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: 2.12 (0.53), residues: 269 helix: 2.05 (0.36), residues: 223 sheet: None (None), residues: 0 loop : -1.91 (0.83), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 286 TYR 0.013 0.001 TYR R 222 PHE 0.007 0.001 PHE R 183 TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 2295) covalent geometry : angle 0.55472 / 0.27 ( 3131) SS BOND : bond 0.00036 / 0.02 ( 2) SS BOND : angle 0.47232 / 0.34 ( 4) hydrogen bonds : bond 0.03954 / 2.57 ( 169) hydrogen bonds : angle 3.91239 / 2.71 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.075 Fit side-chains REVERT: R 38 LEU cc_start: 0.9094 (tp) cc_final: 0.8782 (tp) REVERT: R 75 ASP cc_start: 0.8945 (m-30) cc_final: 0.8604 (t0) REVERT: R 109 MET cc_start: 0.8811 (ttp) cc_final: 0.8501 (ttm) REVERT: R 163 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8544 (tt) REVERT: R 166 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8385 (tptt) REVERT: R 181 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: R 201 SER cc_start: 0.9334 (m) cc_final: 0.8970 (p) REVERT: R 242 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8949 (pp30) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.0429 time to fit residues: 2.1199 Evaluate side-chains 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 242 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081377 restraints weight = 3682.909| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.22 r_work: 0.2827 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2297 Z= 0.113 Angle : 0.536 6.804 3135 Z= 0.261 Chirality : 0.040 0.206 368 Planarity : 0.003 0.028 361 Dihedral : 8.795 57.192 323 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.32 % Allowed : 26.14 % Favored : 70.54 % 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: 2.45 (0.53), residues: 269 helix: 2.44 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.07 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 143 TYR 0.013 0.001 TYR R 222 PHE 0.007 0.001 PHE R 64 TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 2295) covalent geometry : angle 0.53601 / 0.26 ( 3131) SS BOND : bond 0.00020 / 0.01 ( 2) SS BOND : angle 0.40678 / 0.29 ( 4) hydrogen bonds : bond 0.03841 / 2.49 ( 169) hydrogen bonds : angle 3.85042 / 2.68 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.051 Fit side-chains REVERT: R 38 LEU cc_start: 0.8912 (tp) cc_final: 0.8647 (tp) REVERT: R 75 ASP cc_start: 0.8882 (m-30) cc_final: 0.8509 (t0) REVERT: R 109 MET cc_start: 0.8856 (ttp) cc_final: 0.8519 (ttm) REVERT: R 163 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8332 (tt) REVERT: R 166 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8362 (tptt) REVERT: R 201 SER cc_start: 0.9189 (m) cc_final: 0.8681 (p) REVERT: R 242 GLN cc_start: 0.9217 (pp30) cc_final: 0.8859 (pp30) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.0343 time to fit residues: 1.6935 Evaluate side-chains 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.0870 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082438 restraints weight = 3699.096| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.26 r_work: 0.2833 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2297 Z= 0.110 Angle : 0.518 6.601 3135 Z= 0.251 Chirality : 0.039 0.189 368 Planarity : 0.003 0.027 361 Dihedral : 8.630 58.676 323 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.90 % Allowed : 26.14 % Favored : 70.95 % 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 are not related in a simple way. whole: 2.66 (0.52), residues: 269 helix: 2.59 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.01 (0.78), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 143 TYR 0.012 0.002 TYR R 222 PHE 0.007 0.001 PHE R 64 TRP 0.004 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 2295) covalent geometry : angle 0.51809 / 0.25 ( 3131) SS BOND : bond 0.00050 / 0.03 ( 2) SS BOND : angle 0.34678 / 0.24 ( 4) hydrogen bonds : bond 0.03759 / 2.45 ( 169) hydrogen bonds : angle 3.77591 / 2.63 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.083 Fit side-chains REVERT: R 38 LEU cc_start: 0.8905 (tp) cc_final: 0.8656 (tp) REVERT: R 109 MET cc_start: 0.8841 (ttp) cc_final: 0.8486 (ttm) REVERT: R 163 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8341 (tt) REVERT: R 166 LYS cc_start: 0.8973 (ttpp) cc_final: 0.8363 (tptt) REVERT: R 201 SER cc_start: 0.9164 (m) cc_final: 0.8649 (p) REVERT: R 242 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8864 (pp30) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.0369 time to fit residues: 1.9230 Evaluate side-chains 43 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 242 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.079973 restraints weight = 3737.790| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.26 r_work: 0.2797 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2297 Z= 0.147 Angle : 0.542 6.866 3135 Z= 0.266 Chirality : 0.041 0.206 368 Planarity : 0.003 0.027 361 Dihedral : 8.613 56.153 323 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 26.14 % Favored : 70.95 % 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 are not related in a simple way. whole: 2.80 (0.52), residues: 269 helix: 2.67 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.87 (0.80), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 143 TYR 0.013 0.002 TYR R 279 PHE 0.006 0.001 PHE R 239 TRP 0.005 0.001 TRP R 243 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 2295) covalent geometry : angle 0.54167 / 0.27 ( 3131) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 0.49504 / 0.35 ( 4) hydrogen bonds : bond 0.03977 / 2.58 ( 169) hydrogen bonds : angle 3.80716 / 2.63 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.081 Fit side-chains REVERT: R 38 LEU cc_start: 0.8919 (tp) cc_final: 0.8620 (tp) REVERT: R 75 ASP cc_start: 0.8887 (m-30) cc_final: 0.8560 (t0) REVERT: R 109 MET cc_start: 0.8914 (ttp) cc_final: 0.8591 (ttm) REVERT: R 143 ARG cc_start: 0.8468 (ptt-90) cc_final: 0.8126 (ptm-80) REVERT: R 166 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8389 (tptt) REVERT: R 201 SER cc_start: 0.9264 (m) cc_final: 0.8731 (p) REVERT: R 242 GLN cc_start: 0.9168 (pp30) cc_final: 0.8883 (pp30) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0522 time to fit residues: 2.6297 Evaluate side-chains 41 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.080728 restraints weight = 3703.852| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.29 r_work: 0.2803 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2297 Z= 0.127 Angle : 0.540 6.835 3135 Z= 0.265 Chirality : 0.041 0.205 368 Planarity : 0.003 0.027 361 Dihedral : 8.355 55.772 323 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.90 % Allowed : 27.39 % Favored : 69.71 % 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: 2.86 (0.52), residues: 269 helix: 2.71 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.83 (0.80), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 143 TYR 0.012 0.002 TYR R 279 PHE 0.006 0.001 PHE R 244 TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 2295) covalent geometry : angle 0.54020 / 0.27 ( 3131) SS BOND : bond 0.00041 / 0.02 ( 2) SS BOND : angle 0.46991 / 0.32 ( 4) hydrogen bonds : bond 0.03878 / 2.54 ( 169) hydrogen bonds : angle 3.77745 / 2.62 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.091 Fit side-chains REVERT: R 38 LEU cc_start: 0.8918 (tp) cc_final: 0.8620 (tp) REVERT: R 75 ASP cc_start: 0.8904 (m-30) cc_final: 0.8566 (t0) REVERT: R 109 MET cc_start: 0.8902 (ttp) cc_final: 0.8573 (ttm) REVERT: R 143 ARG cc_start: 0.8455 (ptt-90) cc_final: 0.8116 (ptm-80) REVERT: R 166 LYS cc_start: 0.9005 (ttpp) cc_final: 0.8357 (tptt) REVERT: R 201 SER cc_start: 0.9246 (m) cc_final: 0.8729 (p) REVERT: R 242 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8863 (pp30) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.0536 time to fit residues: 2.6267 Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 242 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080892 restraints weight = 3794.143| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.28 r_work: 0.2811 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2297 Z= 0.121 Angle : 0.533 6.791 3135 Z= 0.262 Chirality : 0.040 0.202 368 Planarity : 0.003 0.027 361 Dihedral : 8.261 55.982 323 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.73 % Allowed : 26.56 % Favored : 69.71 % 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: 2.93 (0.53), residues: 269 helix: 2.75 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.80 (0.80), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 143 TYR 0.011 0.002 TYR R 222 PHE 0.005 0.001 PHE R 64 TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 2295) covalent geometry : angle 0.53344 / 0.26 ( 3131) SS BOND : bond 0.00023 / 0.01 ( 2) SS BOND : angle 0.43785 / 0.30 ( 4) hydrogen bonds : bond 0.03834 / 2.51 ( 169) hydrogen bonds : angle 3.78023 / 2.63 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.050 Fit side-chains REVERT: R 38 LEU cc_start: 0.8918 (tp) cc_final: 0.8621 (tp) REVERT: R 75 ASP cc_start: 0.8907 (m-30) cc_final: 0.8560 (t0) REVERT: R 109 MET cc_start: 0.8906 (ttp) cc_final: 0.8566 (ttm) REVERT: R 143 ARG cc_start: 0.8454 (ptt-90) cc_final: 0.8118 (ptm-80) REVERT: R 163 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8352 (tt) REVERT: R 166 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8336 (tptt) REVERT: R 201 SER cc_start: 0.9242 (m) cc_final: 0.8729 (p) REVERT: R 242 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8873 (pp30) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.0334 time to fit residues: 1.6899 Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 242 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.080810 restraints weight = 3794.488| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.26 r_work: 0.2816 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2297 Z= 0.126 Angle : 0.546 6.789 3135 Z= 0.267 Chirality : 0.041 0.201 368 Planarity : 0.003 0.027 361 Dihedral : 8.226 55.962 323 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.49 % Allowed : 27.80 % Favored : 69.71 % 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: 2.89 (0.53), residues: 269 helix: 2.74 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.87 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 143 TYR 0.011 0.002 TYR R 279 PHE 0.005 0.001 PHE R 64 TRP 0.004 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 2295) covalent geometry : angle 0.54657 / 0.27 ( 3131) SS BOND : bond 0.00037 / 0.02 ( 2) SS BOND : angle 0.45384 / 0.32 ( 4) hydrogen bonds : bond 0.03853 / 2.52 ( 169) hydrogen bonds : angle 3.78210 / 2.64 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.050 Fit side-chains REVERT: R 38 LEU cc_start: 0.8949 (tp) cc_final: 0.8660 (tp) REVERT: R 75 ASP cc_start: 0.8926 (m-30) cc_final: 0.8588 (t0) REVERT: R 109 MET cc_start: 0.8904 (ttp) cc_final: 0.8563 (ttm) REVERT: R 143 ARG cc_start: 0.8422 (ptt-90) cc_final: 0.8114 (ptm-80) REVERT: R 166 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8383 (tptt) REVERT: R 201 SER cc_start: 0.9285 (m) cc_final: 0.8804 (p) REVERT: R 242 GLN cc_start: 0.9204 (pp30) cc_final: 0.8967 (pp30) outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 0.0327 time to fit residues: 1.5331 Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081338 restraints weight = 3760.073| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.25 r_work: 0.2820 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2297 Z= 0.119 Angle : 0.534 6.655 3135 Z= 0.261 Chirality : 0.040 0.190 368 Planarity : 0.003 0.027 361 Dihedral : 7.928 55.103 323 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 27.80 % Favored : 69.29 % 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: 2.98 (0.53), residues: 269 helix: 2.80 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.83 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 143 TYR 0.011 0.002 TYR R 279 PHE 0.006 0.001 PHE R 64 TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 2295) covalent geometry : angle 0.53433 / 0.26 ( 3131) SS BOND : bond 0.00031 / 0.02 ( 2) SS BOND : angle 0.41530 / 0.29 ( 4) hydrogen bonds : bond 0.03781 / 2.48 ( 169) hydrogen bonds : angle 3.75753 / 2.62 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 715.10 seconds wall clock time: 12 minutes 51.97 seconds (771.97 seconds total)