Starting phenix.real_space_refine on Fri May 9 13:48:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfd_60057/05_2025/8zfd_60057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfd_60057/05_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_60057/05_2025/8zfd_60057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfd_60057/05_2025/8zfd_60057.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfd_60057/05_2025/8zfd_60057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfd_60057/05_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-5687/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: 2.22, per 1000 atoms: 1.00 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: 0.57 Conformation dependent library (CDL) restraints added in 285.2 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: 0.19 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: 0.45 Time building geometry restraints manager: 0.66 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: 1.280 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- 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 2298 Z= 0.301 Angle : 0.985 19.110 3149 Z= 0.533 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 Details of bonding type rmsd hydrogen bonds : bond 0.11613 ( 148) hydrogen bonds : angle 6.48963 ( 438) SS BOND : bond 0.02350 ( 1) SS BOND : angle 2.57596 ( 2) covalent geometry : bond 0.00655 ( 2297) covalent geometry : angle 0.98362 ( 3147) *********************** 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 : 0.247 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: 1.2048 time to fit residues: 46.8735 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 : 0.232 ------------------------------------------------------------------------------- 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: 0.3980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.180485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130599 restraints weight = 2480.244| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.60 r_work: 0.3514 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2298 Z= 0.180 Angle : 0.706 7.615 3149 Z= 0.363 Chirality : 0.044 0.160 367 Planarity : 0.005 0.038 389 Dihedral : 6.050 27.779 319 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % 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: -1.12 (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 0.009 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 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 148) hydrogen bonds : angle 5.41061 ( 438) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.91314 ( 2) covalent geometry : bond 0.00433 ( 2297) covalent geometry : angle 0.70584 ( 3147) *********************** 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 : 0.255 Fit side-chains REVERT: R 292 ASN cc_start: 0.7351 (p0) cc_final: 0.7087 (p0) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 1.0179 time to fit residues: 34.6263 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 : 0.257 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 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: 0.1980 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132378 restraints weight = 2460.430| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.58 r_work: 0.3535 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2298 Z= 0.143 Angle : 0.640 5.823 3149 Z= 0.329 Chirality : 0.041 0.125 367 Planarity : 0.004 0.038 389 Dihedral : 5.612 27.937 319 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.76 % Allowed : 13.82 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.50), residues: 292 helix: 0.67 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.33 (0.57), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 75 HIS 0.002 0.001 HIS R 271 PHE 0.026 0.002 PHE R 28 TYR 0.019 0.002 TYR R 104 ARG 0.003 0.000 ARG R 226 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 148) hydrogen bonds : angle 5.18812 ( 438) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.68704 ( 2) covalent geometry : bond 0.00340 ( 2297) covalent geometry : angle 0.63964 ( 3147) *********************** 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 43 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.230 Fit side-chains REVERT: R 49 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6597 (tpm-80) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.9060 time to fit residues: 35.5471 Evaluate side-chains 37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.182605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133545 restraints weight = 2444.877| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.58 r_work: 0.3549 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2298 Z= 0.138 Angle : 0.629 5.695 3149 Z= 0.324 Chirality : 0.041 0.128 367 Planarity : 0.004 0.037 389 Dihedral : 5.458 27.834 319 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.61 % Allowed : 13.82 % Favored : 81.57 % 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: -0.28 (0.51), residues: 292 helix: 0.92 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.20 (0.59), 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 0.014 0.002 PHE R 174 TYR 0.019 0.002 TYR R 104 ARG 0.002 0.000 ARG R 187 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 148) hydrogen bonds : angle 5.11057 ( 438) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.67669 ( 2) covalent geometry : bond 0.00325 ( 2297) covalent geometry : angle 0.62877 ( 3147) *********************** 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 42 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.245 Fit side-chains REVERT: R 49 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6471 (tpm-80) REVERT: R 80 LEU cc_start: 0.7964 (mt) cc_final: 0.7536 (mt) outliers start: 10 outliers final: 4 residues processed: 36 average time/residue: 0.8710 time to fit residues: 32.3957 Evaluate side-chains 35 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 49 ARG Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.182091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132750 restraints weight = 2496.293| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.59 r_work: 0.3541 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2298 Z= 0.141 Angle : 0.636 7.011 3149 Z= 0.324 Chirality : 0.041 0.129 367 Planarity : 0.004 0.034 389 Dihedral : 5.416 28.042 319 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.69 % Allowed : 17.05 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.51), residues: 292 helix: 1.09 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.16 (0.62), 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 157 PHE 0.022 0.002 PHE R 28 TYR 0.018 0.002 TYR R 104 ARG 0.002 0.000 ARG R 187 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 148) hydrogen bonds : angle 5.09842 ( 438) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.77199 ( 2) covalent geometry : bond 0.00335 ( 2297) covalent geometry : angle 0.63552 ( 3147) *********************** 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 39 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.252 Fit side-chains REVERT: R 80 LEU cc_start: 0.7936 (mt) cc_final: 0.7699 (mt) outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 0.8818 time to fit residues: 31.9712 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 : 0.244 ------------------------------------------------------------------------------- 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 176 MET Chi-restraints excluded: chain R residue 212 SER 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: 0.9990 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 overall best weight: 0.1384 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.185623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.136560 restraints weight = 2471.654| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.60 r_work: 0.3584 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2298 Z= 0.110 Angle : 0.592 6.489 3149 Z= 0.299 Chirality : 0.039 0.125 367 Planarity : 0.004 0.035 389 Dihedral : 5.053 27.091 319 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.23 % Allowed : 19.82 % 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: 0.17 (0.53), residues: 292 helix: 1.20 (0.38), residues: 217 sheet: None (None), residues: 0 loop : -3.23 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 75 HIS 0.003 0.001 HIS R 157 PHE 0.012 0.001 PHE R 174 TYR 0.014 0.001 TYR R 104 ARG 0.001 0.000 ARG R 187 Details of bonding type rmsd hydrogen bonds : bond 0.02767 ( 148) hydrogen bonds : angle 4.90022 ( 438) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.66988 ( 2) covalent geometry : bond 0.00248 ( 2297) covalent geometry : angle 0.59209 ( 3147) *********************** 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 40 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.245 Fit side-chains REVERT: R 80 LEU cc_start: 0.7978 (mt) cc_final: 0.7734 (mt) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.8323 time to fit residues: 31.0027 Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.0970 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 24 optimal weight: 0.0870 chunk 18 optimal weight: 0.1980 overall best weight: 0.1756 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.184837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135247 restraints weight = 2405.712| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.59 r_work: 0.3566 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2298 Z= 0.116 Angle : 0.594 6.313 3149 Z= 0.299 Chirality : 0.039 0.119 367 Planarity : 0.004 0.035 389 Dihedral : 4.996 26.560 319 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.61 % Allowed : 20.28 % Favored : 75.12 % 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: 0.32 (0.53), residues: 292 helix: 1.31 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.21 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 75 HIS 0.003 0.001 HIS R 157 PHE 0.023 0.002 PHE R 28 TYR 0.016 0.001 TYR R 104 ARG 0.001 0.000 ARG R 187 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 148) hydrogen bonds : angle 4.88872 ( 438) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.59101 ( 2) covalent geometry : bond 0.00265 ( 2297) covalent geometry : angle 0.59440 ( 3147) *********************** 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 42 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.243 Fit side-chains REVERT: R 274 LEU cc_start: 0.8389 (tm) cc_final: 0.8134 (tp) outliers start: 10 outliers final: 4 residues processed: 36 average time/residue: 0.7975 time to fit residues: 29.7779 Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 247 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: 0.0570 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.183434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133487 restraints weight = 2448.074| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.61 r_work: 0.3546 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2298 Z= 0.130 Angle : 0.610 6.175 3149 Z= 0.308 Chirality : 0.040 0.117 367 Planarity : 0.004 0.034 389 Dihedral : 5.059 26.631 319 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.69 % Allowed : 21.66 % Favored : 74.65 % 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: 0.40 (0.52), residues: 292 helix: 1.32 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.07 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 42 HIS 0.004 0.001 HIS R 81 PHE 0.012 0.002 PHE R 174 TYR 0.016 0.002 TYR R 104 ARG 0.001 0.000 ARG R 49 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 148) hydrogen bonds : angle 4.93726 ( 438) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.59892 ( 2) covalent geometry : bond 0.00307 ( 2297) covalent geometry : angle 0.60959 ( 3147) *********************** 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: 8 poor density : 30 time to evaluate : 0.230 Fit side-chains REVERT: R 80 LEU cc_start: 0.8000 (mt) cc_final: 0.7665 (mt) REVERT: R 274 LEU cc_start: 0.8422 (tm) cc_final: 0.8168 (tp) outliers start: 8 outliers final: 4 residues processed: 34 average time/residue: 0.8411 time to fit residues: 29.5826 Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 247 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: 0.5980 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 0.0060 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.183690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134003 restraints weight = 2394.458| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.60 r_work: 0.3549 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2298 Z= 0.127 Angle : 0.604 6.319 3149 Z= 0.306 Chirality : 0.040 0.118 367 Planarity : 0.004 0.036 389 Dihedral : 5.024 26.671 319 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.15 % Allowed : 21.66 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.52), residues: 292 helix: 1.37 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.06 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 75 HIS 0.005 0.001 HIS R 81 PHE 0.026 0.002 PHE R 28 TYR 0.017 0.002 TYR R 104 ARG 0.001 0.000 ARG R 49 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 148) hydrogen bonds : angle 4.85973 ( 438) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.61969 ( 2) covalent geometry : bond 0.00299 ( 2297) covalent geometry : angle 0.60385 ( 3147) *********************** 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 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.278 Fit side-chains REVERT: R 80 LEU cc_start: 0.7986 (mt) cc_final: 0.7653 (mt) REVERT: R 274 LEU cc_start: 0.8404 (tm) cc_final: 0.8144 (tp) outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.8061 time to fit residues: 30.1122 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 : 0.247 ------------------------------------------------------------------------------- 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 247 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: 0.7980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 13 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 4 optimal weight: 0.0770 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.0470 overall best weight: 0.0994 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.187224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138031 restraints weight = 2446.890| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.61 r_work: 0.3612 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2298 Z= 0.106 Angle : 0.578 6.460 3149 Z= 0.290 Chirality : 0.038 0.119 367 Planarity : 0.004 0.036 389 Dihedral : 4.726 25.245 319 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.76 % Allowed : 23.04 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.53), residues: 292 helix: 1.53 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -3.10 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 75 HIS 0.006 0.001 HIS R 81 PHE 0.011 0.001 PHE R 174 TYR 0.015 0.001 TYR R 104 ARG 0.001 0.000 ARG R 187 Details of bonding type rmsd hydrogen bonds : bond 0.02572 ( 148) hydrogen bonds : angle 4.66783 ( 438) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.64319 ( 2) covalent geometry : bond 0.00236 ( 2297) covalent geometry : angle 0.57778 ( 3147) ********************** 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 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.254 Fit side-chains REVERT: R 80 LEU cc_start: 0.7974 (mt) cc_final: 0.7637 (mt) REVERT: R 193 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6697 (tp) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 0.7582 time to fit residues: 29.1921 Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 193 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: 1.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.178944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128849 restraints weight = 2440.679| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.57 r_work: 0.3484 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2298 Z= 0.260 Angle : 0.718 7.015 3149 Z= 0.371 Chirality : 0.047 0.132 367 Planarity : 0.005 0.034 389 Dihedral : 5.575 28.520 319 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.23 % Allowed : 23.50 % 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: -0.02 (0.51), residues: 292 helix: 1.01 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -3.19 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 42 HIS 0.005 0.002 HIS R 82 PHE 0.027 0.003 PHE R 28 TYR 0.022 0.003 TYR R 203 ARG 0.003 0.001 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 148) hydrogen bonds : angle 5.36742 ( 438) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.71769 ( 2) covalent geometry : bond 0.00631 ( 2297) covalent geometry : angle 0.71837 ( 3147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.80 seconds wall clock time: 44 minutes 38.28 seconds (2678.28 seconds total)