Starting phenix.real_space_refine on Wed Jul 1 21:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vv4_32137/07_2026/7vv4_32137.cif" } resolution = 2.97 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 1483 2.51 5 N 338 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 2181 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2101 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.81, per 1000 atoms: 0.37 Number of scatterers: 2181 At special positions: 0 Unit cell: (66.276, 73.64, 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 342 8.00 N 338 7.00 C 1483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 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: 0.19 Conformation dependent library (CDL) restraints added in 81.5 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'R' and resid 27 through 57 removed outlier: 3.691A pdb=" N ILE R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.657A pdb=" N LEU R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.618A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.650A 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 removed outlier: 3.508A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 168 " --> pdb=" O GLU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 213 removed outlier: 3.898A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 244 removed outlier: 4.300A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 251 removed outlier: 3.799A pdb=" N TRP R 248 " --> pdb=" O PHE R 244 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 259 removed outlier: 4.020A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 280 removed outlier: 3.947A pdb=" N VAL R 263 " --> pdb=" O HIS R 259 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 159 hydrogen bonds defined for protein. 477 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: 0.20 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 400 1.33 - 1.45: 605 1.45 - 1.58: 1221 1.58 - 1.70: 1 1.70 - 1.82: 22 Bond restraints: 2249 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.621 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C HIS R 261 " pdb=" O HIS R 261 " ideal model delta sigma weight residual 1.244 1.217 0.027 9.80e-03 1.04e+04 7.64e+00 bond pdb=" C ASN R 271 " pdb=" O ASN R 271 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.89e+00 bond pdb=" N PHE R 76 " pdb=" CA PHE R 76 " ideal model delta sigma weight residual 1.459 1.432 0.027 1.19e-02 7.06e+03 5.26e+00 bond pdb=" C LEU R 267 " pdb=" O LEU R 267 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.19e+00 ... (remaining 2244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 2921 2.50 - 5.01: 111 5.01 - 7.51: 27 7.51 - 10.02: 6 10.02 - 12.52: 2 Bond angle restraints: 3067 Sorted by residual: angle pdb=" N LEU R 256 " pdb=" CA LEU R 256 " pdb=" C LEU R 256 " ideal model delta sigma weight residual 111.14 120.33 -9.19 1.08e+00 8.57e-01 7.24e+01 angle pdb=" N SER R 253 " pdb=" CA SER R 253 " pdb=" C SER R 253 " ideal model delta sigma weight residual 111.28 119.10 -7.82 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N ILE R 260 " pdb=" CA ILE R 260 " pdb=" C ILE R 260 " ideal model delta sigma weight residual 110.72 117.16 -6.44 1.01e+00 9.80e-01 4.07e+01 angle pdb=" N ILE R 249 " pdb=" CA ILE R 249 " pdb=" C ILE R 249 " ideal model delta sigma weight residual 110.72 116.86 -6.14 1.01e+00 9.80e-01 3.70e+01 angle pdb=" N ILE R 246 " pdb=" CA ILE R 246 " pdb=" C ILE R 246 " ideal model delta sigma weight residual 110.72 116.82 -6.10 1.01e+00 9.80e-01 3.65e+01 ... (remaining 3062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 1073 14.13 - 28.25: 129 28.25 - 42.37: 50 42.37 - 56.49: 8 56.49 - 70.61: 3 Dihedral angle restraints: 1263 sinusoidal: 486 harmonic: 777 Sorted by residual: dihedral pdb=" C PHE L 25 " pdb=" N PHE L 25 " pdb=" CA PHE L 25 " pdb=" CB PHE L 25 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" N PHE L 26 " pdb=" C PHE L 26 " pdb=" CA PHE L 26 " pdb=" CB PHE L 26 " ideal model delta harmonic sigma weight residual 122.80 139.84 -17.04 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" C PHE L 26 " pdb=" N PHE L 26 " pdb=" CA PHE L 26 " pdb=" CB PHE L 26 " ideal model delta harmonic sigma weight residual -122.60 -139.42 16.82 0 2.50e+00 1.60e-01 4.53e+01 ... (remaining 1260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 344 0.157 - 0.313: 13 0.313 - 0.470: 3 0.470 - 0.627: 1 0.627 - 0.783: 1 Chirality restraints: 362 Sorted by residual: chirality pdb=" CA PHE L 26 " pdb=" N PHE L 26 " pdb=" C PHE L 26 " pdb=" CB PHE L 26 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PHE L 25 " pdb=" N PHE L 25 " pdb=" C PHE L 25 " pdb=" CB PHE L 25 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" CA HIS R 261 " pdb=" N HIS R 261 " pdb=" C HIS R 261 " pdb=" CB HIS R 261 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 359 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 32 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO R 33 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 241 " -0.010 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C ILE R 241 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 241 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN R 242 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 30 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C THR R 30 " 0.022 2.00e-02 2.50e+03 pdb=" O THR R 30 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU R 31 " -0.007 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 4 2.26 - 2.92: 866 2.92 - 3.58: 3261 3.58 - 4.24: 4665 4.24 - 4.90: 8093 Nonbonded interactions: 16889 Sorted by model distance: nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 1.600 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP R 75 " pdb=" CB SER R 272 " model vdw 2.247 3.440 nonbonded pdb=" CB SER R 177 " pdb=" SG CYS L 22 " model vdw 2.259 3.800 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.309 3.040 ... (remaining 16884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.250 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.950 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.007 0.086 2250 Z= 0.384 Angle : 1.197 12.523 3069 Z= 0.708 Chirality : 0.091 0.783 362 Planarity : 0.006 0.069 356 Dihedral : 14.565 70.611 756 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.75 % Allowed : 4.58 % Favored : 91.67 % Cbeta Deviations : 0.79 % 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: -0.53 (0.49), residues: 265 helix: 0.47 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -3.09 (0.60), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 61 TYR 0.011 0.003 TYR R 279 PHE 0.016 0.002 PHE L 26 TRP 0.009 0.001 TRP R 250 HIS 0.004 0.002 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.38 ( 2249) covalent geometry : angle 1.19675 / 0.71 ( 3067) SS BOND : bond 0.00877 / 0.55 ( 1) SS BOND : angle 1.44231 / 0.65 ( 2) hydrogen bonds : bond 0.16297 / 10.32 ( 159) hydrogen bonds : angle 5.84259 / 4.26 ( 477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.047 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.1966 time to fit residues: 10.6173 Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain L residue 26 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.0040 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0570 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.146568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118638 restraints weight = 3150.040| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.71 r_work: 0.3575 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2250 Z= 0.128 Angle : 0.630 8.065 3069 Z= 0.299 Chirality : 0.040 0.294 362 Planarity : 0.004 0.050 356 Dihedral : 6.869 54.504 301 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.17 % Allowed : 13.33 % Favored : 82.50 % 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: 1.13 (0.51), residues: 265 helix: 1.84 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -3.44 (0.61), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 61 TYR 0.008 0.002 TYR R 113 PHE 0.018 0.001 PHE R 257 TRP 0.025 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 2249) covalent geometry : angle 0.62944 / 0.30 ( 3067) SS BOND : bond 0.00243 / 0.15 ( 1) SS BOND : angle 0.83896 / 0.37 ( 2) hydrogen bonds : bond 0.04191 / 2.71 ( 159) hydrogen bonds : angle 3.75949 / 2.67 ( 477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.048 Fit side-chains REVERT: R 163 LEU cc_start: 0.7955 (mp) cc_final: 0.7637 (tt) REVERT: R 176 ASP cc_start: 0.7696 (p0) cc_final: 0.7374 (p0) REVERT: R 222 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6732 (p90) REVERT: R 242 GLN cc_start: 0.8649 (pp30) cc_final: 0.8434 (pp30) REVERT: R 248 TRP cc_start: 0.7520 (m100) cc_final: 0.7156 (m100) outliers start: 10 outliers final: 3 residues processed: 56 average time/residue: 0.1918 time to fit residues: 11.1691 Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.143752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.115308 restraints weight = 3185.617| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.72 r_work: 0.3538 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2250 Z= 0.130 Angle : 0.621 8.934 3069 Z= 0.287 Chirality : 0.041 0.291 362 Planarity : 0.003 0.043 356 Dihedral : 5.184 47.441 294 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.58 % Allowed : 20.00 % Favored : 75.42 % 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: 1.85 (0.52), residues: 265 helix: 2.28 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.75 (0.63), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 138 TYR 0.010 0.002 TYR R 222 PHE 0.017 0.001 PHE L 25 TRP 0.012 0.001 TRP R 248 HIS 0.002 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 2249) covalent geometry : angle 0.62091 / 0.29 ( 3067) SS BOND : bond 0.00243 / 0.15 ( 1) SS BOND : angle 0.49747 / 0.18 ( 2) hydrogen bonds : bond 0.04056 / 2.63 ( 159) hydrogen bonds : angle 3.53995 / 2.52 ( 477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.079 Fit side-chains REVERT: R 28 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6723 (tmtm) REVERT: R 37 ILE cc_start: 0.7528 (mm) cc_final: 0.7015 (mt) REVERT: R 163 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7570 (tt) REVERT: R 222 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6861 (p90) REVERT: R 242 GLN cc_start: 0.8708 (pp30) cc_final: 0.8496 (pp30) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.2097 time to fit residues: 12.2271 Evaluate side-chains 55 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.142452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.114847 restraints weight = 3191.029| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.66 r_work: 0.3532 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2250 Z= 0.132 Angle : 0.602 10.017 3069 Z= 0.280 Chirality : 0.041 0.290 362 Planarity : 0.003 0.038 356 Dihedral : 4.989 45.976 294 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.25 % Allowed : 23.33 % Favored : 70.42 % 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: 2.26 (0.52), residues: 265 helix: 2.51 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.45 (0.65), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 60 TYR 0.010 0.002 TYR R 222 PHE 0.020 0.001 PHE L 25 TRP 0.011 0.001 TRP R 248 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 2249) covalent geometry : angle 0.60242 / 0.28 ( 3067) SS BOND : bond 0.00281 / 0.18 ( 1) SS BOND : angle 0.30508 / 0.11 ( 2) hydrogen bonds : bond 0.04049 / 2.64 ( 159) hydrogen bonds : angle 3.44634 / 2.44 ( 477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.054 Fit side-chains REVERT: R 28 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6756 (tmtm) REVERT: R 86 CYS cc_start: 0.8092 (m) cc_final: 0.7155 (p) REVERT: R 163 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7516 (tt) REVERT: R 216 LEU cc_start: 0.8564 (mp) cc_final: 0.8020 (mp) REVERT: R 222 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6940 (p90) outliers start: 15 outliers final: 5 residues processed: 56 average time/residue: 0.2522 time to fit residues: 14.6716 Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.141868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114934 restraints weight = 3197.334| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.64 r_work: 0.3525 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2250 Z= 0.132 Angle : 0.602 8.571 3069 Z= 0.283 Chirality : 0.042 0.288 362 Planarity : 0.003 0.036 356 Dihedral : 4.923 45.513 294 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.67 % Allowed : 25.00 % Favored : 68.33 % 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: 2.26 (0.52), residues: 265 helix: 2.49 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.33 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 60 TYR 0.010 0.002 TYR R 222 PHE 0.021 0.001 PHE L 25 TRP 0.030 0.001 TRP R 248 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 2249) covalent geometry : angle 0.60196 / 0.28 ( 3067) SS BOND : bond 0.00283 / 0.18 ( 1) SS BOND : angle 0.70365 / 0.29 ( 2) hydrogen bonds : bond 0.04002 / 2.63 ( 159) hydrogen bonds : angle 3.46776 / 2.46 ( 477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.078 Fit side-chains REVERT: R 28 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6702 (tmtm) REVERT: R 86 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7059 (p) REVERT: R 216 LEU cc_start: 0.8551 (mp) cc_final: 0.8286 (mp) REVERT: R 222 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7001 (p90) outliers start: 16 outliers final: 6 residues processed: 53 average time/residue: 0.2737 time to fit residues: 15.0614 Evaluate side-chains 55 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.144277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117089 restraints weight = 3125.224| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.67 r_work: 0.3556 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2250 Z= 0.120 Angle : 0.645 10.511 3069 Z= 0.291 Chirality : 0.043 0.281 362 Planarity : 0.003 0.037 356 Dihedral : 4.839 45.491 294 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.17 % Allowed : 28.33 % Favored : 67.50 % 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: 265 helix: 2.62 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.30 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 138 TYR 0.010 0.002 TYR R 222 PHE 0.027 0.001 PHE L 25 TRP 0.024 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 2249) covalent geometry : angle 0.64419 / 0.29 ( 3067) SS BOND : bond 0.00312 / 0.20 ( 1) SS BOND : angle 1.01010 / 0.45 ( 2) hydrogen bonds : bond 0.03778 / 2.49 ( 159) hydrogen bonds : angle 3.49915 / 2.48 ( 477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.083 Fit side-chains REVERT: R 28 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6741 (tmtm) REVERT: R 216 LEU cc_start: 0.8551 (mp) cc_final: 0.8210 (mp) REVERT: R 222 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6876 (p90) REVERT: R 250 TRP cc_start: 0.7301 (OUTLIER) cc_final: 0.6676 (m-90) outliers start: 10 outliers final: 6 residues processed: 49 average time/residue: 0.3123 time to fit residues: 15.8807 Evaluate side-chains 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 251 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 0.0070 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.142610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115563 restraints weight = 3178.468| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.73 r_work: 0.3539 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2250 Z= 0.130 Angle : 0.641 10.064 3069 Z= 0.295 Chirality : 0.045 0.283 362 Planarity : 0.003 0.037 356 Dihedral : 4.791 44.523 294 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.00 % Allowed : 28.75 % Favored : 66.25 % 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 (0.53), residues: 265 helix: 2.63 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -2.47 (0.68), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 60 TYR 0.011 0.002 TYR R 222 PHE 0.034 0.001 PHE L 25 TRP 0.012 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 2249) covalent geometry : angle 0.64107 / 0.29 ( 3067) SS BOND : bond 0.00268 / 0.17 ( 1) SS BOND : angle 1.06236 / 0.43 ( 2) hydrogen bonds : bond 0.03948 / 2.60 ( 159) hydrogen bonds : angle 3.49222 / 2.47 ( 477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.085 Fit side-chains REVERT: R 28 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6684 (tmtm) REVERT: R 201 SER cc_start: 0.8238 (m) cc_final: 0.7950 (p) REVERT: R 222 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6932 (p90) REVERT: R 250 TRP cc_start: 0.7197 (OUTLIER) cc_final: 0.6380 (m-90) REVERT: R 251 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6479 (mmtm) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 0.3094 time to fit residues: 15.4166 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.141824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114733 restraints weight = 3160.365| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.76 r_work: 0.3536 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2250 Z= 0.132 Angle : 0.643 8.291 3069 Z= 0.300 Chirality : 0.044 0.282 362 Planarity : 0.003 0.037 356 Dihedral : 4.841 44.726 294 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.25 % Allowed : 29.17 % Favored : 64.58 % 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: 2.42 (0.53), residues: 265 helix: 2.68 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.66 (0.68), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 60 TYR 0.010 0.002 TYR R 222 PHE 0.005 0.001 PHE R 183 TRP 0.011 0.001 TRP R 243 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 2249) covalent geometry : angle 0.64262 / 0.30 ( 3067) SS BOND : bond 0.00092 / 0.06 ( 1) SS BOND : angle 0.99434 / 0.36 ( 2) hydrogen bonds : bond 0.03924 / 2.59 ( 159) hydrogen bonds : angle 3.48448 / 2.46 ( 477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: R 163 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7344 (tt) REVERT: R 201 SER cc_start: 0.8311 (m) cc_final: 0.8044 (p) REVERT: R 222 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6978 (p90) REVERT: R 250 TRP cc_start: 0.7140 (OUTLIER) cc_final: 0.6337 (m-90) outliers start: 15 outliers final: 6 residues processed: 50 average time/residue: 0.2756 time to fit residues: 14.3780 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.0020 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.143321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.116111 restraints weight = 3209.402| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.73 r_work: 0.3552 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2250 Z= 0.126 Angle : 0.654 10.624 3069 Z= 0.301 Chirality : 0.044 0.295 362 Planarity : 0.003 0.037 356 Dihedral : 4.785 44.805 294 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.64 % Favored : 96.98 % Rotamer: Outliers : 4.58 % Allowed : 30.42 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.41 (0.53), residues: 265 helix: 2.68 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.68 (0.68), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 138 TYR 0.010 0.002 TYR R 222 PHE 0.010 0.001 PHE R 76 TRP 0.009 0.001 TRP R 243 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 2249) covalent geometry : angle 0.65383 / 0.30 ( 3067) SS BOND : bond 0.00121 / 0.08 ( 1) SS BOND : angle 0.90235 / 0.34 ( 2) hydrogen bonds : bond 0.03835 / 2.54 ( 159) hydrogen bonds : angle 3.51633 / 2.48 ( 477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: R 163 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7247 (tt) REVERT: R 201 SER cc_start: 0.8227 (m) cc_final: 0.7935 (p) REVERT: R 222 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6953 (p90) REVERT: R 251 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6380 (mmtm) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.2399 time to fit residues: 12.4948 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114029 restraints weight = 3077.930| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.70 r_work: 0.3506 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2250 Z= 0.147 Angle : 0.679 10.365 3069 Z= 0.316 Chirality : 0.046 0.301 362 Planarity : 0.004 0.041 356 Dihedral : 4.848 44.057 294 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.64 % Favored : 96.98 % Rotamer: Outliers : 4.58 % Allowed : 30.83 % Favored : 64.58 % 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: 2.31 (0.53), residues: 265 helix: 2.63 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.76 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 60 TYR 0.011 0.002 TYR R 222 PHE 0.035 0.001 PHE L 25 TRP 0.010 0.001 TRP R 248 HIS 0.003 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 2249) covalent geometry : angle 0.67888 / 0.32 ( 3067) SS BOND : bond 0.00075 / 0.05 ( 1) SS BOND : angle 1.04925 / 0.37 ( 2) hydrogen bonds : bond 0.04106 / 2.72 ( 159) hydrogen bonds : angle 3.59445 / 2.52 ( 477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: R 163 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7359 (tt) REVERT: R 201 SER cc_start: 0.8261 (m) cc_final: 0.7981 (p) REVERT: R 222 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6945 (p90) REVERT: R 251 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6384 (mmtm) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.2904 time to fit residues: 15.0835 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113385 restraints weight = 3280.074| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.79 r_work: 0.3503 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2250 Z= 0.147 Angle : 0.673 10.240 3069 Z= 0.316 Chirality : 0.046 0.298 362 Planarity : 0.003 0.039 356 Dihedral : 4.838 43.804 294 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.02 % Favored : 96.60 % Rotamer: Outliers : 4.58 % Allowed : 30.83 % Favored : 64.58 % 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: 2.28 (0.53), residues: 265 helix: 2.60 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.79 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 60 TYR 0.010 0.002 TYR R 222 PHE 0.010 0.001 PHE R 76 TRP 0.010 0.001 TRP R 154 HIS 0.003 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 2249) covalent geometry : angle 0.67282 / 0.32 ( 3067) SS BOND : bond 0.00080 / 0.05 ( 1) SS BOND : angle 1.05910 / 0.37 ( 2) hydrogen bonds : bond 0.04102 / 2.72 ( 159) hydrogen bonds : angle 3.59416 / 2.53 ( 477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 861.88 seconds wall clock time: 15 minutes 23.75 seconds (923.75 seconds total)