Starting phenix.real_space_refine on Tue Mar 3 10:53:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv0_32133/03_2026/7vv0_32133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv0_32133/03_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_32133/03_2026/7vv0_32133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv0_32133/03_2026/7vv0_32133.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv0_32133/03_2026/7vv0_32133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv0_32133/03_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-5986/lib/python3.9/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: 0.69, per 1000 atoms: 0.32 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: 0.20 Conformation dependent library (CDL) restraints added in 119.8 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: 0.06 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: 0.32 Time building geometry restraints manager: 0.27 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: 1071 11.66 - 23.31: 162 23.31 - 34.96: 59 34.96 - 46.61: 20 46.61 - 58.26: 9 Dihedral angle restraints: 1321 sinusoidal: 547 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 1318 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.220 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 14.054 56.619 813 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 covalent geometry : bond 0.00995 ( 2241) covalent geometry : angle 1.49109 ( 3054) SS BOND : bond 0.00278 ( 2) SS BOND : angle 2.41261 ( 4) hydrogen bonds : bond 0.12596 ( 166) hydrogen bonds : angle 7.50134 ( 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 : 0.072 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.0958 time to fit residues: 3.2297 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 : 0.077 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.170589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143715 restraints weight = 2311.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147424 restraints weight = 1383.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149990 restraints weight = 1021.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150549 restraints weight = 848.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151811 restraints weight = 796.263| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1800 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= 0.125 Angle : 0.645 6.916 3058 Z= 0.318 Chirality : 0.044 0.338 361 Planarity : 0.006 0.046 354 Dihedral : 9.434 59.109 366 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.93 % Allowed : 5.86 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.49), residues: 264 helix: 0.56 (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 0.001 ARG R 140 TYR 0.003 0.001 TYR R 89 PHE 0.011 0.001 PHE R 81 TRP 0.007 0.001 TRP R 133 HIS 0.001 0.001 HIS R 144 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2241) covalent geometry : angle 0.64543 ( 3054) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.55508 ( 4) hydrogen bonds : bond 0.03924 ( 166) hydrogen bonds : angle 4.45809 ( 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 35 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.046 Fit side-chains REVERT: R 287 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6504 (tmtt) outliers start: 7 outliers final: 4 residues processed: 33 average time/residue: 0.0839 time to fit residues: 3.1845 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 : 0.078 ------------------------------------------------------------------------------- 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: 0.1980 chunk 26 optimal weight: 0.0010 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136640 restraints weight = 2365.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140040 restraints weight = 1450.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142304 restraints weight = 1082.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143634 restraints weight = 909.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143661 restraints weight = 819.259| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2243 Z= 0.109 Angle : 0.573 5.718 3058 Z= 0.278 Chirality : 0.043 0.307 361 Planarity : 0.005 0.039 354 Dihedral : 7.667 56.935 356 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.18 % Allowed : 9.21 % Favored : 86.61 % 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: 1.56 (0.53), residues: 264 helix: 1.73 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.80 (0.73), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 140 TYR 0.009 0.001 TYR R 279 PHE 0.009 0.001 PHE R 81 TRP 0.005 0.001 TRP L 13 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2241) covalent geometry : angle 0.57291 ( 3054) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.27608 ( 4) hydrogen bonds : bond 0.03468 ( 166) hydrogen bonds : angle 3.98631 ( 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 30 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.055 Fit side-chains REVERT: R 285 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: R 287 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6361 (tmtt) outliers start: 10 outliers final: 4 residues processed: 27 average time/residue: 0.0794 time to fit residues: 2.4790 Evaluate side-chains 27 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 285 PHE 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: 1.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.0010 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.170549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143245 restraints weight = 2249.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146644 restraints weight = 1332.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149326 restraints weight = 991.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.150655 restraints weight = 819.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151592 restraints weight = 737.404| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2536 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= 0.117 Angle : 0.557 5.769 3058 Z= 0.271 Chirality : 0.041 0.290 361 Planarity : 0.004 0.037 354 Dihedral : 7.276 56.300 356 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.18 % Allowed : 12.13 % Favored : 83.68 % 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: 2.03 (0.53), residues: 264 helix: 2.07 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.57 (0.75), residues: 55 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 81 TRP 0.003 0.001 TRP R 154 HIS 0.000 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2241) covalent geometry : angle 0.55735 ( 3054) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.32873 ( 4) hydrogen bonds : bond 0.03725 ( 166) hydrogen bonds : angle 3.92967 ( 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 35 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.075 Fit side-chains REVERT: R 285 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: R 287 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6371 (tmtt) outliers start: 10 outliers final: 7 residues processed: 30 average time/residue: 0.0799 time to fit residues: 2.7448 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 : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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 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: 0.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142797 restraints weight = 2217.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146449 restraints weight = 1327.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149080 restraints weight = 982.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150454 restraints weight = 810.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150454 restraints weight = 732.097| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2733 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= 0.118 Angle : 0.560 6.306 3058 Z= 0.271 Chirality : 0.041 0.272 361 Planarity : 0.004 0.035 354 Dihedral : 7.290 58.392 356 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 : 4.60 % Allowed : 14.64 % 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: 2.26 (0.54), residues: 264 helix: 2.19 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.34 (0.79), 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 0.017 0.001 PHE R 257 TRP 0.003 0.001 TRP R 190 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2241) covalent geometry : angle 0.56069 ( 3054) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.23633 ( 4) hydrogen bonds : bond 0.03643 ( 166) hydrogen bonds : angle 3.88398 ( 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 32 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.077 Fit side-chains REVERT: R 285 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: R 287 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6346 (tmtt) outliers start: 11 outliers final: 8 residues processed: 27 average time/residue: 0.0818 time to fit residues: 2.5563 Evaluate side-chains 31 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141489 restraints weight = 2225.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145214 restraints weight = 1339.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147573 restraints weight = 989.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148936 restraints weight = 824.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149201 restraints weight = 741.109| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2805 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= 0.126 Angle : 0.569 5.942 3058 Z= 0.275 Chirality : 0.041 0.272 361 Planarity : 0.004 0.035 354 Dihedral : 7.280 59.266 356 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.60 % Allowed : 16.32 % Favored : 79.08 % 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 (0.54), residues: 264 helix: 2.21 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.28 (0.79), 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 0.012 0.001 PHE R 257 TRP 0.004 0.001 TRP R 190 HIS 0.000 0.000 HIS R 259 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2241) covalent geometry : angle 0.56939 ( 3054) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.28220 ( 4) hydrogen bonds : bond 0.03782 ( 166) hydrogen bonds : angle 3.90542 ( 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 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.075 Fit side-chains REVERT: R 285 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: R 287 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6442 (tmtt) outliers start: 11 outliers final: 8 residues processed: 32 average time/residue: 0.0760 time to fit residues: 2.8047 Evaluate side-chains 35 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141093 restraints weight = 2289.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144907 restraints weight = 1359.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146986 restraints weight = 1004.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148665 restraints weight = 844.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148717 restraints weight = 751.698| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2865 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= 0.128 Angle : 0.566 5.836 3058 Z= 0.276 Chirality : 0.041 0.266 361 Planarity : 0.004 0.034 354 Dihedral : 7.292 59.887 356 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.44 % Allowed : 15.90 % 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: 2.32 (0.53), residues: 264 helix: 2.18 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.11 (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 0.012 0.001 PHE R 257 TRP 0.004 0.001 TRP R 190 HIS 0.001 0.000 HIS R 259 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2241) covalent geometry : angle 0.56677 ( 3054) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.26725 ( 4) hydrogen bonds : bond 0.03784 ( 166) hydrogen bonds : angle 3.89759 ( 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 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.070 Fit side-chains REVERT: R 285 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: R 287 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6394 (tmtt) outliers start: 13 outliers final: 9 residues processed: 34 average time/residue: 0.0894 time to fit residues: 3.4414 Evaluate side-chains 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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 Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141733 restraints weight = 2239.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145389 restraints weight = 1336.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147834 restraints weight = 984.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149248 restraints weight = 818.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149488 restraints weight = 740.161| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2930 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= 0.120 Angle : 0.557 5.885 3058 Z= 0.273 Chirality : 0.041 0.253 361 Planarity : 0.004 0.034 354 Dihedral : 7.182 58.164 356 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.02 % Allowed : 16.32 % 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: 2.29 (0.54), residues: 264 helix: 2.12 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -1.37 (0.86), residues: 48 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 0.019 0.001 PHE R 257 TRP 0.003 0.001 TRP R 190 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2241) covalent geometry : angle 0.55683 ( 3054) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.26211 ( 4) hydrogen bonds : bond 0.03690 ( 166) hydrogen bonds : angle 3.86863 ( 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 32 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.077 Fit side-chains REVERT: R 285 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6479 (m-80) outliers start: 12 outliers final: 9 residues processed: 27 average time/residue: 0.0875 time to fit residues: 2.7601 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 : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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: 0.6980 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134215 restraints weight = 2329.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137603 restraints weight = 1376.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140018 restraints weight = 1020.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140842 restraints weight = 843.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141846 restraints weight = 783.796| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3103 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= 0.112 Angle : 0.542 5.745 3058 Z= 0.266 Chirality : 0.040 0.226 361 Planarity : 0.004 0.033 354 Dihedral : 6.730 54.723 352 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.18 % Allowed : 16.74 % Favored : 79.08 % 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 (0.54), residues: 264 helix: 2.23 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -1.31 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.006 0.001 TYR R 113 PHE 0.018 0.001 PHE R 257 TRP 0.004 0.001 TRP L 13 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 2241) covalent geometry : angle 0.54261 ( 3054) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.18775 ( 4) hydrogen bonds : bond 0.03530 ( 166) hydrogen bonds : angle 3.81010 ( 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 32 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.049 Fit side-chains REVERT: R 248 TRP cc_start: 0.7520 (m100) cc_final: 0.7311 (m100) REVERT: R 285 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6325 (m-80) outliers start: 10 outliers final: 9 residues processed: 27 average time/residue: 0.0806 time to fit residues: 2.4662 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 : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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: 1.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132283 restraints weight = 2357.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135601 restraints weight = 1410.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137681 restraints weight = 1041.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139044 restraints weight = 868.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139044 restraints weight = 776.654| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3055 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= 0.143 Angle : 0.587 6.014 3058 Z= 0.287 Chirality : 0.043 0.246 361 Planarity : 0.005 0.055 354 Dihedral : 6.923 56.967 352 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.60 % Allowed : 17.15 % 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: 2.28 (0.54), residues: 264 helix: 2.11 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -1.36 (0.86), residues: 48 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 0.018 0.001 PHE R 257 TRP 0.005 0.001 TRP R 190 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2241) covalent geometry : angle 0.58766 ( 3054) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.30373 ( 4) hydrogen bonds : bond 0.03989 ( 166) hydrogen bonds : angle 3.97189 ( 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 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.044 Fit side-chains REVERT: R 285 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6456 (m-80) outliers start: 11 outliers final: 8 residues processed: 31 average time/residue: 0.0415 time to fit residues: 1.5299 Evaluate side-chains 33 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 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 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133266 restraints weight = 2350.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136321 restraints weight = 1440.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138437 restraints weight = 1091.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139066 restraints weight = 918.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140141 restraints weight = 861.591| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3128 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 : 0.556 5.798 3058 Z= 0.275 Chirality : 0.041 0.232 361 Planarity : 0.005 0.051 354 Dihedral : 6.778 54.182 352 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 2.30 (0.54), residues: 264 helix: 2.13 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -1.37 (0.86), residues: 48 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 0.018 0.001 PHE R 257 TRP 0.004 0.001 TRP L 13 HIS 0.001 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 2241) covalent geometry : angle 0.55607 ( 3054) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.27221 ( 4) hydrogen bonds : bond 0.03733 ( 166) hydrogen bonds : angle 3.86628 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 587.50 seconds wall clock time: 10 minutes 46.95 seconds (646.95 seconds total)