Starting phenix.real_space_refine on Wed Jul 1 21:06:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbg_38217/07_2026/8xbg_38217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbg_38217/07_2026/8xbg_38217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xbg_38217/07_2026/8xbg_38217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbg_38217/07_2026/8xbg_38217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbg_38217/07_2026/8xbg_38217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbg_38217/07_2026/8xbg_38217.map" } resolution = 3.43 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 ------------------------------------------------------------------------------- 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= -0.024 sd= 0.464 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 22 5.16 5 C 1637 2.51 5 N 399 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2461 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'KW0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.89, per 1000 atoms: 0.36 Number of scatterers: 2461 At special positions: 0 Unit cell: (75.956, 64.786, 70.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 1 15.00 O 402 8.00 N 399 7.00 C 1637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 299 " distance=2.06 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 204 " distance=2.10 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: 0.31 Conformation dependent library (CDL) restraints added in 131.0 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 9 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 'A' and resid 50 through 81 Processing helix chain 'A' and resid 87 through 117 Proline residue: A 108 - end of helix removed outlier: 4.285A pdb=" N GLN A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 157 removed outlier: 4.157A pdb=" N TYR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.515A pdb=" N LYS A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 removed outlier: 4.168A pdb=" N ASN A 212 " --> pdb=" O ASP A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 213 through 252 removed outlier: 3.765A pdb=" N ALA A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 294 removed outlier: 3.543A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Proline residue: A 281 - end of helix removed outlier: 4.395A pdb=" N PHE A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 331 removed outlier: 3.790A pdb=" N LYS A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 331 through 342 199 hydrogen bonds defined for protein. 597 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: 0.42 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 397 1.31 - 1.44: 653 1.44 - 1.57: 1423 1.57 - 1.70: 7 1.70 - 1.83: 34 Bond restraints: 2514 Sorted by residual: bond pdb=" CA SER A 268 " pdb=" CB SER A 268 " ideal model delta sigma weight residual 1.529 1.430 0.099 1.55e-02 4.16e+03 4.05e+01 bond pdb=" C TYR A 135 " pdb=" O TYR A 135 " ideal model delta sigma weight residual 1.237 1.299 -0.063 1.19e-02 7.06e+03 2.79e+01 bond pdb=" C SER A 141 " pdb=" N ILE A 142 " ideal model delta sigma weight residual 1.334 1.277 0.057 1.26e-02 6.30e+03 2.08e+01 bond pdb=" C ARG A 152 " pdb=" O ARG A 152 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.17e-02 7.31e+03 1.98e+01 bond pdb=" C LEU A 145 " pdb=" O LEU A 145 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.83e+01 ... (remaining 2509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 2831 1.91 - 3.83: 501 3.83 - 5.74: 51 5.74 - 7.65: 6 7.65 - 9.57: 1 Bond angle restraints: 3390 Sorted by residual: angle pdb=" NE ARG A 152 " pdb=" CZ ARG A 152 " pdb=" NH1 ARG A 152 " ideal model delta sigma weight residual 121.50 116.50 5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" N ILE A 290 " pdb=" CA ILE A 290 " pdb=" C ILE A 290 " ideal model delta sigma weight residual 110.72 106.30 4.42 1.01e+00 9.80e-01 1.91e+01 angle pdb=" C PRO A 281 " pdb=" CA PRO A 281 " pdb=" CB PRO A 281 " ideal model delta sigma weight residual 113.20 105.86 7.34 1.69e+00 3.50e-01 1.89e+01 angle pdb=" O ILE A 241 " pdb=" C ILE A 241 " pdb=" N GLY A 242 " ideal model delta sigma weight residual 121.87 126.07 -4.20 9.70e-01 1.06e+00 1.88e+01 angle pdb=" CA PHE A 269 " pdb=" C PHE A 269 " pdb=" O PHE A 269 " ideal model delta sigma weight residual 119.97 115.02 4.95 1.15e+00 7.56e-01 1.85e+01 ... (remaining 3385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 1429 24.55 - 49.10: 75 49.10 - 73.65: 6 73.65 - 98.20: 4 98.20 - 122.75: 2 Dihedral angle restraints: 1516 sinusoidal: 634 harmonic: 882 Sorted by residual: dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual -86.00 -5.52 -80.48 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" C15 KW0 A 401 " pdb=" C16 KW0 A 401 " pdb=" C17 KW0 A 401 " pdb=" C18 KW0 A 401 " ideal model delta sinusoidal sigma weight residual 190.27 67.52 122.75 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C11 KW0 A 401 " pdb=" C12 KW0 A 401 " pdb=" C13 KW0 A 401 " pdb=" C14 KW0 A 401 " ideal model delta sinusoidal sigma weight residual 175.32 -65.66 -119.02 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 1513 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.106: 327 0.106 - 0.211: 68 0.211 - 0.316: 4 0.316 - 0.422: 0 0.422 - 0.527: 2 Chirality restraints: 401 Sorted by residual: chirality pdb=" CB ILE A 142 " pdb=" CA ILE A 142 " pdb=" CG1 ILE A 142 " pdb=" CG2 ILE A 142 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" C20 KW0 A 401 " pdb=" C19 KW0 A 401 " pdb=" C21 KW0 A 401 " pdb=" O4 KW0 A 401 " both_signs ideal model delta sigma weight residual False -2.15 -2.62 0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" CB ILE A 290 " pdb=" CA ILE A 290 " pdb=" CG1 ILE A 290 " pdb=" CG2 ILE A 290 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 398 not shown) Planarity restraints: 397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 KW0 A 401 " 0.121 2.00e-02 2.50e+03 9.19e-02 8.44e+01 pdb=" C11 KW0 A 401 " -0.047 2.00e-02 2.50e+03 pdb=" C8 KW0 A 401 " 0.047 2.00e-02 2.50e+03 pdb=" C9 KW0 A 401 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 269 " 0.057 2.00e-02 2.50e+03 3.96e-02 2.75e+01 pdb=" CG PHE A 269 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 269 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE A 269 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 269 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 PHE A 269 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 269 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 92 " 0.045 2.00e-02 2.50e+03 3.53e-02 2.49e+01 pdb=" CG TYR A 92 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR A 92 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 92 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 92 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 92 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 92 " -0.014 2.00e-02 2.50e+03 ... (remaining 394 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 170 2.74 - 3.28: 2744 3.28 - 3.82: 3911 3.82 - 4.36: 4866 4.36 - 4.90: 8079 Nonbonded interactions: 19770 Sorted by model distance: nonbonded pdb=" OG SER A 54 " pdb=" O HIS A 114 " model vdw 2.198 3.040 nonbonded pdb=" O LYS A 254 " pdb=" OG SER A 258 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASN A 244 " pdb=" NH2 ARG A 247 " model vdw 2.233 3.120 nonbonded pdb=" O MET A 203 " pdb=" NH2 ARG A 208 " model vdw 2.257 3.120 nonbonded pdb=" O LYS A 155 " pdb=" OG SER A 159 " model vdw 2.294 3.040 ... (remaining 19765 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: 0.090 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.600 Find NCS groups from input model: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 0.015 0.099 2516 Z= 1.073 Angle : 1.450 9.567 3394 Z= 1.013 Chirality : 0.089 0.527 401 Planarity : 0.011 0.092 397 Dihedral : 15.730 122.745 940 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.36 % Allowed : 2.91 % Favored : 96.73 % 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: 0.00 (0.43), residues: 296 helix: 0.67 (0.29), residues: 237 sheet: None (None), residues: 0 loop : -2.57 (0.62), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG A 152 TYR 0.081 0.013 TYR A 92 PHE 0.058 0.013 PHE A 269 TRP 0.047 0.009 TRP A 179 HIS 0.013 0.004 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.01542 / 1.07 ( 2514) covalent geometry : angle 1.45049 / 1.01 ( 3390) SS BOND : bond 0.05192 / 2.50 ( 2) SS BOND : angle 0.71497 / 0.36 ( 4) hydrogen bonds : bond 0.10165 / 6.45 ( 199) hydrogen bonds : angle 5.15180 / 3.85 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.087 Fit side-chains REVERT: A 250 LYS cc_start: 0.7426 (tptm) cc_final: 0.7032 (ptmt) REVERT: A 260 LYS cc_start: 0.7126 (pttm) cc_final: 0.6168 (tttp) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0781 time to fit residues: 4.2429 Evaluate side-chains 43 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.203145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163569 restraints weight = 2552.351| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.20 r_work: 0.3705 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2516 Z= 0.158 Angle : 0.587 5.483 3394 Z= 0.315 Chirality : 0.040 0.133 401 Planarity : 0.004 0.044 397 Dihedral : 12.455 117.744 365 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.45 % Allowed : 12.36 % Favored : 86.18 % 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: 1.23 (0.45), residues: 296 helix: 1.58 (0.31), residues: 240 sheet: None (None), residues: 0 loop : -2.60 (0.64), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 251 TYR 0.011 0.001 TYR A 92 PHE 0.012 0.002 PHE A 186 TRP 0.007 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 2514) covalent geometry : angle 0.58538 / 0.31 ( 3390) SS BOND : bond 0.00300 / 0.15 ( 2) SS BOND : angle 1.28461 / 0.80 ( 4) hydrogen bonds : bond 0.04733 / 3.24 ( 199) hydrogen bonds : angle 4.16694 / 3.10 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.086 Fit side-chains REVERT: A 48 MET cc_start: 0.2197 (ppp) cc_final: 0.1649 (ptm) REVERT: A 104 ILE cc_start: 0.7462 (mp) cc_final: 0.7243 (mp) REVERT: A 250 LYS cc_start: 0.7799 (tptm) cc_final: 0.7302 (ptmt) REVERT: A 251 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7811 (tpp80) REVERT: A 260 LYS cc_start: 0.6713 (pttm) cc_final: 0.5735 (tttp) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0865 time to fit residues: 4.3459 Evaluate side-chains 44 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 211 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.204317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.165408 restraints weight = 2648.584| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.24 r_work: 0.3736 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2516 Z= 0.136 Angle : 0.546 7.730 3394 Z= 0.287 Chirality : 0.038 0.152 401 Planarity : 0.003 0.041 397 Dihedral : 11.274 102.902 365 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.91 % Allowed : 16.36 % Favored : 80.73 % 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: 1.87 (0.47), residues: 296 helix: 2.03 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.53 (0.67), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.009 0.001 TYR A 92 PHE 0.009 0.002 PHE A 231 TRP 0.007 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 2514) covalent geometry : angle 0.54433 / 0.29 ( 3390) SS BOND : bond 0.00165 / 0.09 ( 2) SS BOND : angle 1.32666 / 0.87 ( 4) hydrogen bonds : bond 0.04254 / 2.91 ( 199) hydrogen bonds : angle 3.81116 / 2.83 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.082 Fit side-chains REVERT: A 48 MET cc_start: 0.2057 (ppp) cc_final: 0.1594 (ptm) REVERT: A 104 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7080 (mp) REVERT: A 172 ILE cc_start: 0.7596 (mm) cc_final: 0.7373 (mm) REVERT: A 250 LYS cc_start: 0.7815 (tptm) cc_final: 0.7329 (ptmt) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.0658 time to fit residues: 3.2904 Evaluate side-chains 47 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 298 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.203231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165005 restraints weight = 2637.347| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.21 r_work: 0.3740 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2516 Z= 0.138 Angle : 0.535 6.555 3394 Z= 0.283 Chirality : 0.038 0.160 401 Planarity : 0.004 0.037 397 Dihedral : 10.961 98.388 365 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.64 % Allowed : 17.45 % Favored : 78.91 % 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: 1.88 (0.47), residues: 296 helix: 2.04 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.50 (0.70), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 251 TYR 0.009 0.001 TYR A 92 PHE 0.011 0.002 PHE A 186 TRP 0.006 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 2514) covalent geometry : angle 0.53390 / 0.28 ( 3390) SS BOND : bond 0.00272 / 0.13 ( 2) SS BOND : angle 1.08006 / 0.69 ( 4) hydrogen bonds : bond 0.04248 / 2.92 ( 199) hydrogen bonds : angle 3.77121 / 2.80 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.086 Fit side-chains REVERT: A 48 MET cc_start: 0.2240 (ppp) cc_final: 0.1894 (ptm) REVERT: A 104 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6952 (mp) REVERT: A 172 ILE cc_start: 0.7476 (mm) cc_final: 0.7208 (mm) REVERT: A 250 LYS cc_start: 0.7887 (tptm) cc_final: 0.7329 (ptmt) REVERT: A 260 LYS cc_start: 0.6690 (pttm) cc_final: 0.5688 (tttp) REVERT: A 266 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6666 (ptp-170) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.0886 time to fit residues: 4.5851 Evaluate side-chains 48 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.205236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166562 restraints weight = 2614.754| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.22 r_work: 0.3738 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2516 Z= 0.131 Angle : 0.522 6.248 3394 Z= 0.275 Chirality : 0.038 0.150 401 Planarity : 0.003 0.035 397 Dihedral : 10.440 85.962 365 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.00 % Allowed : 18.55 % Favored : 77.45 % 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: 2.01 (0.48), residues: 296 helix: 2.15 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.57 (0.72), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 251 TYR 0.008 0.001 TYR A 92 PHE 0.009 0.001 PHE A 186 TRP 0.006 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 2514) covalent geometry : angle 0.52155 / 0.27 ( 3390) SS BOND : bond 0.00078 / 0.04 ( 2) SS BOND : angle 1.01770 / 0.66 ( 4) hydrogen bonds : bond 0.04116 / 2.83 ( 199) hydrogen bonds : angle 3.68962 / 2.73 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.052 Fit side-chains REVERT: A 48 MET cc_start: 0.2191 (ppp) cc_final: 0.1859 (ptm) REVERT: A 104 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6945 (mp) REVERT: A 172 ILE cc_start: 0.7475 (mm) cc_final: 0.7201 (mm) REVERT: A 250 LYS cc_start: 0.7967 (tptm) cc_final: 0.7399 (ptmt) REVERT: A 260 LYS cc_start: 0.6738 (pttm) cc_final: 0.5692 (tttp) REVERT: A 266 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6637 (ptp-170) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.0487 time to fit residues: 2.7287 Evaluate side-chains 52 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.200829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161439 restraints weight = 2648.662| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.24 r_work: 0.3683 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2516 Z= 0.160 Angle : 0.556 5.875 3394 Z= 0.295 Chirality : 0.039 0.164 401 Planarity : 0.003 0.033 397 Dihedral : 10.514 80.594 365 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.36 % Allowed : 20.36 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.47), residues: 296 helix: 1.97 (0.31), residues: 241 sheet: None (None), residues: 0 loop : -2.63 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 251 TYR 0.007 0.001 TYR A 92 PHE 0.014 0.002 PHE A 186 TRP 0.005 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 2514) covalent geometry : angle 0.55544 / 0.29 ( 3390) SS BOND : bond 0.00252 / 0.12 ( 2) SS BOND : angle 1.03718 / 0.66 ( 4) hydrogen bonds : bond 0.04505 / 3.09 ( 199) hydrogen bonds : angle 3.83002 / 2.85 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.084 Fit side-chains REVERT: A 104 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6959 (mp) REVERT: A 250 LYS cc_start: 0.7999 (tptm) cc_final: 0.7431 (ptmt) REVERT: A 260 LYS cc_start: 0.6962 (pttm) cc_final: 0.5796 (tttp) REVERT: A 266 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6781 (ptp-170) outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 0.0800 time to fit residues: 4.4489 Evaluate side-chains 48 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.205642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167112 restraints weight = 2652.194| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.23 r_work: 0.3754 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2516 Z= 0.119 Angle : 0.503 5.914 3394 Z= 0.267 Chirality : 0.037 0.134 401 Planarity : 0.003 0.030 397 Dihedral : 9.810 73.236 365 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.00 % Allowed : 21.09 % Favored : 74.91 % 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: 2.29 (0.48), residues: 296 helix: 2.35 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.53 (0.74), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.007 0.001 TYR A 139 PHE 0.006 0.001 PHE A 275 TRP 0.006 0.001 TRP A 228 HIS 0.001 0.000 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 2514) covalent geometry : angle 0.50270 / 0.27 ( 3390) SS BOND : bond 0.00290 / 0.14 ( 2) SS BOND : angle 0.87914 / 0.57 ( 4) hydrogen bonds : bond 0.03915 / 2.66 ( 199) hydrogen bonds : angle 3.61052 / 2.67 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.084 Fit side-chains REVERT: A 104 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6863 (mp) REVERT: A 172 ILE cc_start: 0.7461 (mm) cc_final: 0.7168 (mm) REVERT: A 250 LYS cc_start: 0.7970 (tptm) cc_final: 0.7385 (ptmt) REVERT: A 260 LYS cc_start: 0.6711 (pttm) cc_final: 0.5625 (tttp) REVERT: A 266 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6575 (ptp-170) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.0665 time to fit residues: 3.8079 Evaluate side-chains 50 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.205360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167097 restraints weight = 2655.257| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.22 r_work: 0.3742 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2516 Z= 0.121 Angle : 0.506 5.716 3394 Z= 0.268 Chirality : 0.037 0.136 401 Planarity : 0.003 0.028 397 Dihedral : 9.788 83.821 365 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.73 % Allowed : 20.36 % Favored : 74.91 % 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: 2.36 (0.49), residues: 296 helix: 2.40 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.52 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.007 0.001 TYR A 92 PHE 0.007 0.001 PHE A 186 TRP 0.005 0.001 TRP A 228 HIS 0.001 0.000 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 2514) covalent geometry : angle 0.50539 / 0.27 ( 3390) SS BOND : bond 0.00061 / 0.03 ( 2) SS BOND : angle 0.99563 / 0.64 ( 4) hydrogen bonds : bond 0.03932 / 2.68 ( 199) hydrogen bonds : angle 3.58404 / 2.65 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.088 Fit side-chains REVERT: A 104 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6941 (mp) REVERT: A 111 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7125 (pt) REVERT: A 172 ILE cc_start: 0.7464 (mm) cc_final: 0.7165 (mm) REVERT: A 250 LYS cc_start: 0.7986 (tptm) cc_final: 0.7394 (ptmt) REVERT: A 260 LYS cc_start: 0.6832 (pttm) cc_final: 0.5654 (tttp) REVERT: A 266 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6778 (ptp-170) REVERT: A 312 MET cc_start: 0.7542 (mmt) cc_final: 0.7000 (mmt) outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 0.0796 time to fit residues: 4.4851 Evaluate side-chains 52 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.207662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168737 restraints weight = 2660.812| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.25 r_work: 0.3735 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2516 Z= 0.119 Angle : 0.499 5.679 3394 Z= 0.265 Chirality : 0.037 0.133 401 Planarity : 0.003 0.027 397 Dihedral : 9.524 84.629 365 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 5.09 % Allowed : 20.00 % Favored : 74.91 % 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: 2.43 (0.49), residues: 296 helix: 2.45 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.52 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.006 0.001 TYR A 139 PHE 0.007 0.001 PHE A 186 TRP 0.005 0.001 TRP A 228 HIS 0.001 0.000 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 2514) covalent geometry : angle 0.49837 / 0.26 ( 3390) SS BOND : bond 0.00086 / 0.05 ( 2) SS BOND : angle 0.92466 / 0.58 ( 4) hydrogen bonds : bond 0.03838 / 2.61 ( 199) hydrogen bonds : angle 3.55000 / 2.62 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.053 Fit side-chains REVERT: A 104 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.7005 (mp) REVERT: A 111 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7114 (pt) REVERT: A 172 ILE cc_start: 0.7410 (mm) cc_final: 0.7112 (mm) REVERT: A 250 LYS cc_start: 0.7964 (tptm) cc_final: 0.7358 (ptmt) REVERT: A 260 LYS cc_start: 0.6870 (pttm) cc_final: 0.5637 (tttp) REVERT: A 266 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7060 (ttp-170) outliers start: 14 outliers final: 9 residues processed: 50 average time/residue: 0.0773 time to fit residues: 4.4260 Evaluate side-chains 53 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.207001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167968 restraints weight = 2658.325| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.26 r_work: 0.3764 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2516 Z= 0.115 Angle : 0.507 6.240 3394 Z= 0.265 Chirality : 0.037 0.124 401 Planarity : 0.003 0.026 397 Dihedral : 9.140 80.079 365 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.64 % Allowed : 21.82 % Favored : 74.55 % 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: 2.57 (0.49), residues: 296 helix: 2.57 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.57 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.008 0.001 TYR A 139 PHE 0.006 0.001 PHE A 186 TRP 0.006 0.001 TRP A 228 HIS 0.001 0.000 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 2514) covalent geometry : angle 0.50677 / 0.26 ( 3390) SS BOND : bond 0.00104 / 0.05 ( 2) SS BOND : angle 0.81653 / 0.52 ( 4) hydrogen bonds : bond 0.03765 / 2.55 ( 199) hydrogen bonds : angle 3.50397 / 2.59 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.053 Fit side-chains REVERT: A 104 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.7028 (mp) REVERT: A 111 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7088 (pt) REVERT: A 172 ILE cc_start: 0.7419 (mm) cc_final: 0.7113 (mm) REVERT: A 247 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7668 (ttp-110) REVERT: A 250 LYS cc_start: 0.7967 (tptm) cc_final: 0.7383 (ptmt) REVERT: A 312 MET cc_start: 0.7565 (mmt) cc_final: 0.7013 (mmt) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.0527 time to fit residues: 2.9393 Evaluate side-chains 50 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.210287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.171490 restraints weight = 2646.433| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.22 r_work: 0.3750 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2516 Z= 0.120 Angle : 0.508 5.549 3394 Z= 0.266 Chirality : 0.037 0.132 401 Planarity : 0.003 0.026 397 Dihedral : 8.963 72.791 365 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.36 % Allowed : 21.09 % Favored : 74.55 % 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 (0.49), residues: 296 helix: 2.51 (0.32), residues: 241 sheet: None (None), residues: 0 loop : -2.56 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.007 0.001 TYR A 92 PHE 0.007 0.001 PHE A 186 TRP 0.005 0.001 TRP A 228 HIS 0.001 0.000 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 2514) covalent geometry : angle 0.50791 / 0.27 ( 3390) SS BOND : bond 0.00070 / 0.03 ( 2) SS BOND : angle 0.80971 / 0.52 ( 4) hydrogen bonds : bond 0.03845 / 2.62 ( 199) hydrogen bonds : angle 3.53312 / 2.62 ( 597) =============================================================================== Job complete usr+sys time: 693.14 seconds wall clock time: 12 minutes 36.50 seconds (756.50 seconds total)