Starting phenix.real_space_refine on Wed Mar 5 15:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfd_60057/03_2025/8zfd_60057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfd_60057/03_2025/8zfd_60057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zfd_60057/03_2025/8zfd_60057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfd_60057/03_2025/8zfd_60057.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfd_60057/03_2025/8zfd_60057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfd_60057/03_2025/8zfd_60057.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.014 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 13 5.16 5 C 1475 2.51 5 N 373 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2231 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2231 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 12, 'TRANS': 281} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 114 Time building chain proxies: 2.37, per 1000 atoms: 1.06 Number of scatterers: 2231 At special positions: 0 Unit cell: (61.48, 66.78, 69.96, 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 13 16.00 O 370 8.00 N 373 7.00 C 1475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.05 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: 0.55 Conformation dependent library (CDL) restraints added in 286.8 milliseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.602A pdb=" N PHE R 28 " --> pdb=" O SER R 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Proline residue: R 35 - end of helix removed outlier: 3.705A pdb=" N GLN R 50 " --> pdb=" O ARG R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 70 removed outlier: 3.935A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 81 removed outlier: 4.155A pdb=" N TRP R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP R 77 " --> pdb=" O PRO R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 101 removed outlier: 3.696A pdb=" N SER R 91 " --> pdb=" O HIS R 87 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY R 96 " --> pdb=" O CYS R 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE R 97 " --> pdb=" O LYS R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 123 removed outlier: 3.681A pdb=" N ALA R 108 " --> pdb=" O TYR R 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS R 111 " --> pdb=" O ILE R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 146 Processing helix chain 'R' and resid 152 through 157 removed outlier: 3.580A pdb=" N HIS R 157 " --> pdb=" O PRO R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 191 removed outlier: 3.634A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 213 removed outlier: 3.889A pdb=" N SER R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 256 removed outlier: 3.677A pdb=" N SER R 230 " --> pdb=" O ARG R 226 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 4.060A pdb=" N TYR R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU R 254 " --> pdb=" O SER R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 277 removed outlier: 3.712A pdb=" N GLU R 264 " --> pdb=" O CYS R 260 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG R 265 " --> pdb=" O GLY R 261 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N SER R 268 " --> pdb=" O GLU R 264 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA R 269 " --> pdb=" O ARG R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 280 No H-bonds generated for 'chain 'R' and resid 278 through 280' Processing helix chain 'R' and resid 282 through 290 removed outlier: 3.811A pdb=" N ILE R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 304 148 hydrogen bonds defined for protein. 438 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: 0.55 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 418 1.33 - 1.45: 613 1.45 - 1.57: 1249 1.57 - 1.69: 0 1.69 - 1.82: 17 Bond restraints: 2297 Sorted by residual: bond pdb=" CA CYS R 170 " pdb=" C CYS R 170 " ideal model delta sigma weight residual 1.520 1.489 0.031 1.12e-02 7.97e+03 7.46e+00 bond pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.58e-02 4.01e+03 6.62e+00 bond pdb=" C CYS R 170 " pdb=" O CYS R 170 " ideal model delta sigma weight residual 1.235 1.206 0.028 1.18e-02 7.18e+03 5.73e+00 bond pdb=" CA GLU R 172 " pdb=" CB GLU R 172 " ideal model delta sigma weight residual 1.534 1.500 0.034 1.57e-02 4.06e+03 4.58e+00 bond pdb=" C PHE R 174 " pdb=" N PRO R 175 " ideal model delta sigma weight residual 1.334 1.287 0.047 2.34e-02 1.83e+03 4.09e+00 ... (remaining 2292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 3118 3.82 - 7.64: 24 7.64 - 11.47: 2 11.47 - 15.29: 2 15.29 - 19.11: 1 Bond angle restraints: 3147 Sorted by residual: angle pdb=" N LYS R 173 " pdb=" CA LYS R 173 " pdb=" C LYS R 173 " ideal model delta sigma weight residual 110.80 91.69 19.11 2.13e+00 2.20e-01 8.05e+01 angle pdb=" C LYS R 173 " pdb=" CA LYS R 173 " pdb=" CB LYS R 173 " ideal model delta sigma weight residual 110.42 124.89 -14.47 1.99e+00 2.53e-01 5.29e+01 angle pdb=" C PHE R 174 " pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta sigma weight residual 110.17 121.65 -11.48 1.97e+00 2.58e-01 3.39e+01 angle pdb=" N CYS R 170 " pdb=" CA CYS R 170 " pdb=" C CYS R 170 " ideal model delta sigma weight residual 108.13 100.51 7.62 1.72e+00 3.38e-01 1.96e+01 angle pdb=" C GLU R 172 " pdb=" N LYS R 173 " pdb=" CA LYS R 173 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 ... (remaining 3142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.26: 1117 13.26 - 26.52: 158 26.52 - 39.78: 31 39.78 - 53.03: 8 53.03 - 66.29: 2 Dihedral angle restraints: 1316 sinusoidal: 445 harmonic: 871 Sorted by residual: dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 145.43 -52.43 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" C PHE R 174 " pdb=" N PHE R 174 " pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta harmonic sigma weight residual -122.60 -135.40 12.80 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" CA THR R 216 " pdb=" C THR R 216 " pdb=" N GLU R 217 " pdb=" CA GLU R 217 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 1313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 331 0.089 - 0.177: 34 0.177 - 0.266: 1 0.266 - 0.354: 0 0.354 - 0.443: 1 Chirality restraints: 367 Sorted by residual: chirality pdb=" CA PHE R 174 " pdb=" N PHE R 174 " pdb=" C PHE R 174 " pdb=" CB PHE R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA PHE R 171 " pdb=" N PHE R 171 " pdb=" C PHE R 171 " pdb=" CB PHE R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA CYS R 170 " pdb=" N CYS R 170 " pdb=" C CYS R 170 " pdb=" CB CYS R 170 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 364 not shown) Planarity restraints: 389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 174 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO R 175 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 174 " 0.027 2.00e-02 2.50e+03 2.26e-02 8.91e+00 pdb=" CG PHE R 174 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE R 174 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE R 174 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 174 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE R 174 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE R 174 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 102 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C ASN R 102 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN R 102 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE R 103 " 0.017 2.00e-02 2.50e+03 ... (remaining 386 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 380 2.75 - 3.29: 2172 3.29 - 3.83: 3795 3.83 - 4.36: 4370 4.36 - 4.90: 7602 Nonbonded interactions: 18319 Sorted by model distance: nonbonded pdb=" OH TYR R 45 " pdb=" NH2 ARG R 49 " model vdw 2.217 3.120 nonbonded pdb=" OD1 ASN R 60 " pdb=" NE1 TRP R 144 " model vdw 2.279 3.120 nonbonded pdb=" O LEU R 20 " pdb=" OG SER R 24 " model vdw 2.382 3.040 nonbonded pdb=" O GLY R 149 " pdb=" OG SER R 152 " model vdw 2.443 3.040 nonbonded pdb=" N LYS R 173 " pdb=" O LYS R 173 " model vdw 2.452 2.496 ... (remaining 18314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.140 Find NCS groups from input model: 0.030 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 2297 Z= 0.426 Angle : 0.984 19.110 3147 Z= 0.532 Chirality : 0.055 0.443 367 Planarity : 0.006 0.080 389 Dihedral : 13.008 66.293 749 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.46 % Allowed : 0.92 % Favored : 98.62 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.48), residues: 292 helix: -0.04 (0.37), residues: 202 sheet: None (None), residues: 0 loop : -3.46 (0.54), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 75 HIS 0.004 0.002 HIS R 157 PHE 0.052 0.003 PHE R 174 TYR 0.026 0.003 TYR R 104 ARG 0.005 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.254 Fit side-chains REVERT: R 83 ASP cc_start: 0.6430 (m-30) cc_final: 0.6117 (m-30) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 1.2593 time to fit residues: 48.9881 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.180293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130333 restraints weight = 2479.087| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.61 r_work: 0.3506 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2297 Z= 0.285 Angle : 0.712 7.680 3147 Z= 0.366 Chirality : 0.044 0.163 367 Planarity : 0.005 0.038 389 Dihedral : 6.064 27.804 319 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.92 % Allowed : 12.90 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.49), residues: 292 helix: 0.29 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.50 (0.56), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 PHE 0.023 0.002 PHE R 174 TYR 0.022 0.002 TYR R 104 ARG 0.005 0.001 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.257 Fit side-chains REVERT: R 292 ASN cc_start: 0.7358 (p0) cc_final: 0.7081 (p0) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 1.0644 time to fit residues: 36.1303 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 19 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 3 optimal weight: 0.0010 chunk 1 optimal weight: 0.9990 overall best weight: 0.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.184309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134942 restraints weight = 2421.411| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.60 r_work: 0.3569 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2297 Z= 0.171 Angle : 0.608 5.718 3147 Z= 0.311 Chirality : 0.040 0.121 367 Planarity : 0.004 0.040 389 Dihedral : 5.397 27.005 319 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.23 % Allowed : 12.90 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.50), residues: 292 helix: 0.76 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -3.32 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 75 HIS 0.002 0.001 HIS R 271 PHE 0.026 0.002 PHE R 28 TYR 0.017 0.001 TYR R 104 ARG 0.003 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.272 Fit side-chains REVERT: R 49 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6622 (tpm-80) REVERT: R 80 LEU cc_start: 0.7908 (mt) cc_final: 0.7464 (mt) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.8342 time to fit residues: 34.5006 Evaluate side-chains 37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ARG Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.0070 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132366 restraints weight = 2414.139| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.57 r_work: 0.3519 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2297 Z= 0.235 Angle : 0.644 5.728 3147 Z= 0.333 Chirality : 0.042 0.135 367 Planarity : 0.004 0.036 389 Dihedral : 5.477 28.187 319 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.61 % Allowed : 15.21 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.51), residues: 292 helix: 0.96 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.30 (0.57), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 75 HIS 0.005 0.001 HIS R 157 PHE 0.015 0.002 PHE R 174 TYR 0.020 0.002 TYR R 104 ARG 0.003 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.240 Fit side-chains REVERT: R 80 LEU cc_start: 0.7933 (mt) cc_final: 0.7511 (mt) REVERT: R 152 SER cc_start: 0.8068 (t) cc_final: 0.7439 (p) REVERT: R 274 LEU cc_start: 0.8468 (tm) cc_final: 0.8244 (tp) outliers start: 10 outliers final: 4 residues processed: 37 average time/residue: 0.9517 time to fit residues: 36.3949 Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 212 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.181278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131120 restraints weight = 2442.793| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.61 r_work: 0.3507 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2297 Z= 0.263 Angle : 0.659 7.056 3147 Z= 0.337 Chirality : 0.042 0.131 367 Planarity : 0.004 0.034 389 Dihedral : 5.515 28.645 319 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.53 % Allowed : 17.05 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.51), residues: 292 helix: 0.98 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.19 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 82 PHE 0.022 0.002 PHE R 28 TYR 0.020 0.002 TYR R 104 ARG 0.002 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.254 Fit side-chains REVERT: R 51 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6463 (m90) REVERT: R 80 LEU cc_start: 0.8033 (mt) cc_final: 0.7800 (mt) REVERT: R 152 SER cc_start: 0.8127 (t) cc_final: 0.7285 (p) REVERT: R 274 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8210 (tp) outliers start: 12 outliers final: 5 residues processed: 38 average time/residue: 0.8264 time to fit residues: 32.5366 Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 51 HIS Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.184080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134283 restraints weight = 2434.462| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.59 r_work: 0.3548 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2297 Z= 0.176 Angle : 0.602 6.534 3147 Z= 0.307 Chirality : 0.040 0.123 367 Planarity : 0.004 0.035 389 Dihedral : 5.190 27.775 319 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.15 % Allowed : 18.89 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.52), residues: 292 helix: 1.02 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.11 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 75 HIS 0.003 0.001 HIS R 157 PHE 0.013 0.001 PHE R 174 TYR 0.016 0.001 TYR R 104 ARG 0.002 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.251 Fit side-chains REVERT: R 80 LEU cc_start: 0.7987 (mt) cc_final: 0.7732 (mt) REVERT: R 152 SER cc_start: 0.8135 (t) cc_final: 0.7445 (p) REVERT: R 274 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8166 (tp) outliers start: 9 outliers final: 4 residues processed: 37 average time/residue: 0.8187 time to fit residues: 31.3966 Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 0.0970 overall best weight: 0.0978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.187196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138314 restraints weight = 2469.926| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.61 r_work: 0.3607 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2297 Z= 0.144 Angle : 0.572 6.387 3147 Z= 0.286 Chirality : 0.038 0.123 367 Planarity : 0.004 0.035 389 Dihedral : 4.843 26.114 319 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.76 % Allowed : 21.66 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.52), residues: 292 helix: 1.28 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.08 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 75 HIS 0.003 0.001 HIS R 157 PHE 0.024 0.001 PHE R 28 TYR 0.013 0.001 TYR R 104 ARG 0.002 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.239 Fit side-chains REVERT: R 274 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8096 (tp) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.8654 time to fit residues: 32.3100 Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 22 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 HIS ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132527 restraints weight = 2442.088| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.60 r_work: 0.3534 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2297 Z= 0.225 Angle : 0.641 7.240 3147 Z= 0.322 Chirality : 0.041 0.118 367 Planarity : 0.004 0.035 389 Dihedral : 5.122 27.265 319 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.15 % Allowed : 22.12 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.52), residues: 292 helix: 1.24 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.00 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 42 HIS 0.004 0.001 HIS R 81 PHE 0.013 0.002 PHE R 174 TYR 0.018 0.002 TYR R 104 ARG 0.002 0.000 ARG R 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.248 Fit side-chains REVERT: R 80 LEU cc_start: 0.8025 (mt) cc_final: 0.7691 (mt) REVERT: R 274 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8163 (tp) outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.8275 time to fit residues: 30.8523 Evaluate side-chains 35 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 24 optimal weight: 0.0370 chunk 10 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 HIS ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.187659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138422 restraints weight = 2453.239| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.61 r_work: 0.3615 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 : 0.002 0.033 2297 Z= 0.142 Angle : 0.572 6.530 3147 Z= 0.285 Chirality : 0.038 0.124 367 Planarity : 0.004 0.035 389 Dihedral : 4.712 25.371 319 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.69 % Allowed : 22.58 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.53), residues: 292 helix: 1.49 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.08 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 75 HIS 0.005 0.001 HIS R 81 PHE 0.024 0.001 PHE R 28 TYR 0.015 0.001 TYR R 104 ARG 0.002 0.000 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.256 Fit side-chains REVERT: R 193 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6686 (tp) REVERT: R 274 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8065 (tp) outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.7718 time to fit residues: 28.0649 Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 4 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 HIS ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS R 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.184503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134839 restraints weight = 2399.931| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.60 r_work: 0.3560 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2297 Z= 0.180 Angle : 0.578 5.926 3147 Z= 0.297 Chirality : 0.039 0.116 367 Planarity : 0.004 0.033 389 Dihedral : 4.844 25.207 319 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.69 % Allowed : 23.04 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.53), residues: 292 helix: 1.54 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.06 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 75 HIS 0.005 0.001 HIS R 81 PHE 0.012 0.001 PHE R 174 TYR 0.015 0.002 TYR R 104 ARG 0.001 0.000 ARG R 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.250 Fit side-chains REVERT: R 80 LEU cc_start: 0.8021 (mt) cc_final: 0.7725 (mt) REVERT: R 274 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8107 (tp) outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.8388 time to fit residues: 30.4279 Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 HIS ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.181711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131781 restraints weight = 2396.786| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.60 r_work: 0.3526 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2297 Z= 0.253 Angle : 0.639 5.896 3147 Z= 0.326 Chirality : 0.042 0.123 367 Planarity : 0.004 0.034 389 Dihedral : 5.181 26.901 319 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.15 % Allowed : 23.04 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.52), residues: 292 helix: 1.36 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -2.96 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 42 HIS 0.005 0.001 HIS R 81 PHE 0.023 0.002 PHE R 28 TYR 0.017 0.002 TYR R 104 ARG 0.002 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.73 seconds wall clock time: 46 minutes 24.35 seconds (2784.35 seconds total)