Starting phenix.real_space_refine on Wed Jul 1 21:02:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv0_32133/07_2026/7vv0_32133.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 1477 2.51 5 N 340 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 2175 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2093 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} 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: 0.49, per 1000 atoms: 0.23 Number of scatterers: 2175 At special positions: 0 Unit cell: (65.4594, 72.0882, 61.3164, 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 340 8.00 N 340 7.00 C 1477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.11 Conformation dependent library (CDL) restraints added in 45.8 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 502 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 82.8% 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 30 through 58 removed outlier: 3.523A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.950A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 145 through 166 removed outlier: 4.357A pdb=" N LEU R 163 " --> pdb=" O LEU R 159 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 213 removed outlier: 3.992A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.390A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 274 Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 274 through 280 166 hydrogen bonds defined for protein. 498 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: 0.19 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 299 1.29 - 1.42: 660 1.42 - 1.55: 1251 1.55 - 1.68: 9 1.68 - 1.81: 22 Bond restraints: 2241 Sorted by residual: bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.426 -0.090 1.36e-02 5.41e+03 4.39e+01 bond pdb=" C LEU R 38 " pdb=" O LEU R 38 " ideal model delta sigma weight residual 1.236 1.157 0.080 1.32e-02 5.74e+03 3.64e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.619 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N TRP R 179 " pdb=" CA TRP R 179 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.53e-02 4.27e+03 1.48e+01 ... (remaining 2236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 2910 3.03 - 6.06: 115 6.06 - 9.09: 15 9.09 - 12.11: 12 12.11 - 15.14: 2 Bond angle restraints: 3054 Sorted by residual: angle pdb=" N ARG R 286 " pdb=" CA ARG R 286 " pdb=" C ARG R 286 " ideal model delta sigma weight residual 111.28 123.19 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N SER R 284 " pdb=" CA SER R 284 " pdb=" C SER R 284 " ideal model delta sigma weight residual 112.30 122.92 -10.62 1.36e+00 5.41e-01 6.10e+01 angle pdb=" N TRP R 179 " pdb=" CA TRP R 179 " pdb=" C TRP R 179 " ideal model delta sigma weight residual 113.55 104.34 9.21 1.26e+00 6.30e-01 5.34e+01 angle pdb=" N LYS L 11 " pdb=" CA LYS L 11 " pdb=" C LYS L 11 " ideal model delta sigma weight residual 107.93 119.23 -11.30 1.65e+00 3.67e-01 4.69e+01 angle pdb=" C PHE R 285 " pdb=" N ARG R 286 " pdb=" CA ARG R 286 " ideal model delta sigma weight residual 120.28 127.44 -7.16 1.34e+00 5.57e-01 2.85e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.66: 1028 11.66 - 23.31: 155 23.31 - 34.96: 55 34.96 - 46.61: 20 46.61 - 58.26: 7 Dihedral angle restraints: 1265 sinusoidal: 491 harmonic: 774 Sorted by residual: dihedral pdb=" CB CYS R 26 " pdb=" SG CYS R 26 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual 93.00 151.26 -58.26 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA GLU R 164 " pdb=" C GLU R 164 " pdb=" N GLY R 165 " pdb=" CA GLY R 165 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C ILE R 32 " pdb=" N ILE R 32 " pdb=" CA ILE R 32 " pdb=" CB ILE R 32 " ideal model delta harmonic sigma weight residual -122.00 -132.39 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 1262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 342 0.151 - 0.303: 14 0.303 - 0.454: 3 0.454 - 0.605: 1 0.605 - 0.757: 1 Chirality restraints: 361 Sorted by residual: chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA SER R 284 " pdb=" N SER R 284 " pdb=" C SER R 284 " pdb=" CB SER R 284 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" CA ARG R 286 " pdb=" N ARG R 286 " pdb=" C ARG R 286 " pdb=" CB ARG R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 358 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 37 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ILE R 37 " 0.069 2.00e-02 2.50e+03 pdb=" O ILE R 37 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU R 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL R 149 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 151 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C VAL R 151 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL R 151 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU R 152 " -0.021 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 17 2.59 - 3.16: 1669 3.16 - 3.74: 3446 3.74 - 4.32: 4483 4.32 - 4.90: 7429 Nonbonded interactions: 17044 Sorted by model distance: nonbonded pdb=" CD1 LEU R 38 " pdb=" CD1 ILE R 83 " model vdw 2.007 3.880 nonbonded pdb=" O LYS L 12 " pdb=" CE1 PHE R 257 " model vdw 2.215 3.340 nonbonded pdb=" CZ2 TRP L 13 " pdb=" CH2 TRP R 243 " model vdw 2.304 3.640 nonbonded pdb=" NH1 ARG L 10 " pdb=" OD2 ASP R 184 " model vdw 2.311 3.120 nonbonded pdb=" O SER R 284 " pdb=" OG SER R 284 " model vdw 2.317 3.040 ... (remaining 17039 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 group one per residue 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: 0.500 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: 0.000 Set scattering table: 0.010 Process input model: 2.750 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.090 2243 Z= 0.527 Angle : 1.493 15.143 3058 Z= 0.809 Chirality : 0.091 0.757 361 Planarity : 0.012 0.083 354 Dihedral : 14.094 56.619 757 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.93 % Allowed : 1.67 % Favored : 95.40 % Cbeta Deviations : 0.40 % 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: -3.44 (0.39), residues: 264 helix: -2.01 (0.28), residues: 205 sheet: None (None), residues: 0 loop : -2.48 (0.60), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG R 140 TYR 0.012 0.003 TYR R 279 PHE 0.028 0.003 PHE R 244 TRP 0.014 0.002 TRP R 243 HIS 0.004 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00995 / 0.53 ( 2241) covalent geometry : angle 1.49109 / 0.81 ( 3054) SS BOND : bond 0.00278 / 0.14 ( 2) SS BOND : angle 2.41261 / 1.61 ( 4) hydrogen bonds : bond 0.12596 / 7.64 ( 166) hydrogen bonds : angle 7.50134 / 5.15 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.044 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.0636 time to fit residues: 2.1440 Evaluate side-chains 26 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143786 restraints weight = 2312.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147643 restraints weight = 1384.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149775 restraints weight = 1020.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151582 restraints weight = 857.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152404 restraints weight = 757.809| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2243 Z= 0.128 Angle : 0.645 6.858 3058 Z= 0.319 Chirality : 0.044 0.345 361 Planarity : 0.006 0.046 354 Dihedral : 8.983 59.094 310 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.35 % Allowed : 5.86 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.49), residues: 264 helix: 0.57 (0.34), residues: 210 sheet: None (None), residues: 0 loop : -2.02 (0.73), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 140 TYR 0.004 0.001 TYR R 89 PHE 0.012 0.001 PHE R 81 TRP 0.007 0.001 TRP R 133 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 2241) covalent geometry : angle 0.64537 / 0.32 ( 3054) SS BOND : bond 0.00115 / 0.06 ( 2) SS BOND : angle 0.57617 / 0.42 ( 4) hydrogen bonds : bond 0.03903 / 2.32 ( 166) hydrogen bonds : angle 4.45044 / 3.01 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.044 Fit side-chains REVERT: R 287 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6483 (tmtt) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.0657 time to fit residues: 2.5120 Evaluate side-chains 27 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133475 restraints weight = 2398.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137357 restraints weight = 1360.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139938 restraints weight = 969.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140832 restraints weight = 799.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141984 restraints weight = 732.231| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2243 Z= 0.122 Angle : 0.599 6.383 3058 Z= 0.290 Chirality : 0.044 0.327 361 Planarity : 0.005 0.040 354 Dihedral : 7.035 57.743 300 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.18 % Allowed : 9.62 % Favored : 86.19 % 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: 1.40 (0.52), residues: 264 helix: 1.62 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.87 (0.72), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 140 TYR 0.008 0.001 TYR R 279 PHE 0.009 0.001 PHE R 244 TRP 0.004 0.001 TRP R 133 HIS 0.000 0.000 HIS R 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2241) covalent geometry : angle 0.59973 / 0.29 ( 3054) SS BOND : bond 0.00146 / 0.07 ( 2) SS BOND : angle 0.34432 / 0.28 ( 4) hydrogen bonds : bond 0.03745 / 2.26 ( 166) hydrogen bonds : angle 4.06762 / 2.73 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.045 Fit side-chains REVERT: R 60 ARG cc_start: 0.7461 (ttm110) cc_final: 0.7250 (ttm-80) REVERT: R 287 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6436 (tmtt) outliers start: 10 outliers final: 5 residues processed: 26 average time/residue: 0.0607 time to fit residues: 1.7952 Evaluate side-chains 25 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.0050 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139431 restraints weight = 2272.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143046 restraints weight = 1380.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145116 restraints weight = 1028.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145623 restraints weight = 871.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147212 restraints weight = 822.345| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2243 Z= 0.132 Angle : 0.575 6.707 3058 Z= 0.281 Chirality : 0.042 0.331 361 Planarity : 0.004 0.038 354 Dihedral : 6.747 56.701 300 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.18 % Allowed : 12.55 % Favored : 83.26 % 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: 1.75 (0.53), residues: 264 helix: 1.87 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.74 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 140 TYR 0.006 0.001 TYR R 279 PHE 0.009 0.001 PHE R 244 TRP 0.004 0.001 TRP R 53 HIS 0.000 0.000 HIS R 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 2241) covalent geometry : angle 0.57557 / 0.28 ( 3054) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 0.38218 / 0.27 ( 4) hydrogen bonds : bond 0.03909 / 2.36 ( 166) hydrogen bonds : angle 3.98683 / 2.67 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.043 Fit side-chains REVERT: R 285 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: R 287 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6409 (tmtt) outliers start: 10 outliers final: 7 residues processed: 28 average time/residue: 0.0468 time to fit residues: 1.5285 Evaluate side-chains 31 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.168323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141185 restraints weight = 2238.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.144979 restraints weight = 1342.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147290 restraints weight = 988.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148544 restraints weight = 832.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 13)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148545 restraints weight = 748.472| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2243 Z= 0.121 Angle : 0.572 6.577 3058 Z= 0.275 Chirality : 0.041 0.329 361 Planarity : 0.004 0.036 354 Dihedral : 6.481 55.483 300 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.18 % Allowed : 14.23 % Favored : 81.59 % 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: 2.09 (0.53), residues: 264 helix: 2.07 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.44 (0.77), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.005 0.001 TYR R 279 PHE 0.008 0.001 PHE R 244 TRP 0.003 0.001 TRP R 133 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 2241) covalent geometry : angle 0.57240 / 0.28 ( 3054) SS BOND : bond 0.00115 / 0.06 ( 2) SS BOND : angle 0.28100 / 0.23 ( 4) hydrogen bonds : bond 0.03650 / 2.21 ( 166) hydrogen bonds : angle 3.88207 / 2.60 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.045 Fit side-chains REVERT: R 285 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6367 (m-80) outliers start: 10 outliers final: 7 residues processed: 24 average time/residue: 0.0521 time to fit residues: 1.4527 Evaluate side-chains 27 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132952 restraints weight = 2273.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135861 restraints weight = 1403.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138000 restraints weight = 1064.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138732 restraints weight = 899.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138732 restraints weight = 838.785| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2243 Z= 0.114 Angle : 0.562 6.377 3058 Z= 0.269 Chirality : 0.040 0.324 361 Planarity : 0.004 0.035 354 Dihedral : 6.081 54.721 296 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.18 % Allowed : 15.06 % Favored : 80.75 % 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: 2.30 (0.53), residues: 264 helix: 2.19 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.26 (0.80), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 140 TYR 0.006 0.001 TYR R 113 PHE 0.008 0.001 PHE R 81 TRP 0.003 0.001 TRP R 133 HIS 0.000 0.000 HIS R 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 2241) covalent geometry : angle 0.56230 / 0.27 ( 3054) SS BOND : bond 0.00098 / 0.05 ( 2) SS BOND : angle 0.22678 / 0.20 ( 4) hydrogen bonds : bond 0.03576 / 2.16 ( 166) hydrogen bonds : angle 3.83998 / 2.58 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.057 Fit side-chains REVERT: R 285 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.6225 (m-80) outliers start: 10 outliers final: 8 residues processed: 25 average time/residue: 0.0645 time to fit residues: 1.8551 Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130238 restraints weight = 2352.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133332 restraints weight = 1450.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135374 restraints weight = 1090.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136318 restraints weight = 918.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137207 restraints weight = 845.926| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2243 Z= 0.132 Angle : 0.577 6.532 3058 Z= 0.279 Chirality : 0.041 0.327 361 Planarity : 0.005 0.037 354 Dihedral : 6.199 57.817 296 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.18 % Allowed : 15.90 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.53), residues: 264 helix: 2.16 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -1.09 (0.82), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 140 TYR 0.005 0.001 TYR R 279 PHE 0.008 0.001 PHE R 183 TRP 0.004 0.001 TRP R 190 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 2241) covalent geometry : angle 0.57702 / 0.28 ( 3054) SS BOND : bond 0.00133 / 0.06 ( 2) SS BOND : angle 0.30026 / 0.26 ( 4) hydrogen bonds : bond 0.03816 / 2.31 ( 166) hydrogen bonds : angle 3.90801 / 2.62 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.043 Fit side-chains REVERT: R 285 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.6315 (m-80) outliers start: 10 outliers final: 8 residues processed: 25 average time/residue: 0.0592 time to fit residues: 1.6906 Evaluate side-chains 28 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130110 restraints weight = 2334.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133467 restraints weight = 1391.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134889 restraints weight = 1028.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136539 restraints weight = 904.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136585 restraints weight = 800.634| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2243 Z= 0.142 Angle : 0.586 6.628 3058 Z= 0.284 Chirality : 0.042 0.329 361 Planarity : 0.005 0.049 354 Dihedral : 6.227 57.854 296 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.60 % Allowed : 16.74 % Favored : 78.66 % 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: 264 helix: 2.14 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -1.09 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.004 0.001 TYR R 279 PHE 0.008 0.001 PHE R 183 TRP 0.004 0.001 TRP R 190 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 2241) covalent geometry : angle 0.58585 / 0.28 ( 3054) SS BOND : bond 0.00124 / 0.06 ( 2) SS BOND : angle 0.37137 / 0.30 ( 4) hydrogen bonds : bond 0.03892 / 2.36 ( 166) hydrogen bonds : angle 3.94966 / 2.65 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.043 Fit side-chains REVERT: R 285 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.6338 (m-80) outliers start: 11 outliers final: 8 residues processed: 26 average time/residue: 0.0459 time to fit residues: 1.4088 Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 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 = 0.3860 r_free = 0.3860 target = 0.159017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132498 restraints weight = 2348.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135831 restraints weight = 1384.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138051 restraints weight = 1011.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139334 restraints weight = 843.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139334 restraints weight = 757.453| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2243 Z= 0.127 Angle : 0.573 6.430 3058 Z= 0.278 Chirality : 0.041 0.325 361 Planarity : 0.005 0.043 354 Dihedral : 6.171 59.366 296 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.18 % Allowed : 17.57 % Favored : 78.24 % 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: 2.38 (0.54), residues: 264 helix: 2.22 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.14 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.005 0.001 TYR R 113 PHE 0.008 0.001 PHE R 183 TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 2241) covalent geometry : angle 0.57298 / 0.28 ( 3054) SS BOND : bond 0.00090 / 0.04 ( 2) SS BOND : angle 0.28302 / 0.26 ( 4) hydrogen bonds : bond 0.03712 / 2.25 ( 166) hydrogen bonds : angle 3.88110 / 2.60 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.079 Fit side-chains REVERT: R 285 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6233 (m-80) outliers start: 10 outliers final: 8 residues processed: 25 average time/residue: 0.0802 time to fit residues: 2.3351 Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.159015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133207 restraints weight = 2380.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136103 restraints weight = 1478.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138238 restraints weight = 1118.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139381 restraints weight = 945.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139381 restraints weight = 858.773| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2243 Z= 0.141 Angle : 0.589 6.575 3058 Z= 0.286 Chirality : 0.042 0.327 361 Planarity : 0.005 0.042 354 Dihedral : 6.243 59.947 296 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.77 % Allowed : 18.41 % Favored : 77.82 % 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 (0.54), residues: 264 helix: 2.15 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.15 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.005 0.001 TYR R 222 PHE 0.009 0.001 PHE R 183 TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 2241) covalent geometry : angle 0.58890 / 0.29 ( 3054) SS BOND : bond 0.00120 / 0.06 ( 2) SS BOND : angle 0.33072 / 0.30 ( 4) hydrogen bonds : bond 0.03896 / 2.36 ( 166) hydrogen bonds : angle 3.94945 / 2.65 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.086 Fit side-chains REVERT: R 257 PHE cc_start: 0.7477 (t80) cc_final: 0.7091 (t80) REVERT: R 285 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6266 (m-80) outliers start: 9 outliers final: 8 residues processed: 30 average time/residue: 0.0676 time to fit residues: 2.4285 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.157236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130883 restraints weight = 2366.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134159 restraints weight = 1453.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136043 restraints weight = 1081.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136043 restraints weight = 920.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136043 restraints weight = 920.074| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2243 Z= 0.125 Angle : 0.571 6.331 3058 Z= 0.278 Chirality : 0.041 0.323 361 Planarity : 0.005 0.040 354 Dihedral : 6.055 56.952 296 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.77 % Allowed : 18.83 % Favored : 77.41 % 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 (0.54), residues: 264 helix: 2.25 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.07 (0.86), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.005 0.001 TYR R 113 PHE 0.008 0.001 PHE R 183 TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 2241) covalent geometry : angle 0.57145 / 0.28 ( 3054) SS BOND : bond 0.00093 / 0.05 ( 2) SS BOND : angle 0.28460 / 0.26 ( 4) hydrogen bonds : bond 0.03699 / 2.23 ( 166) hydrogen bonds : angle 3.87260 / 2.59 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 506.42 seconds wall clock time: 9 minutes 21.92 seconds (561.92 seconds total)