Starting phenix.real_space_refine on Fri May 9 14:19:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbi_38219/05_2025/8xbi_38219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbi_38219/05_2025/8xbi_38219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbi_38219/05_2025/8xbi_38219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbi_38219/05_2025/8xbi_38219.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbi_38219/05_2025/8xbi_38219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbi_38219/05_2025/8xbi_38219.cif" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= -0.028 sd= 0.435 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 22 5.16 5 C 1641 2.51 5 N 399 2.21 5 O 404 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: 2467 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'KW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.09, per 1000 atoms: 0.85 Number of scatterers: 2467 At special positions: 0 Unit cell: (64.55, 73.587, 77.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 1 15.00 O 404 8.00 N 399 7.00 C 1641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 299 " distance=2.04 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " distance=2.08 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: 0.67 Conformation dependent library (CDL) restraints added in 269.2 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 84.6% 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 50 through 82 removed outlier: 3.686A pdb=" N ILE R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 117 Proline residue: R 108 - end of helix removed outlier: 4.189A pdb=" N GLN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 157 removed outlier: 3.561A pdb=" N CYS R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 197 removed outlier: 3.702A pdb=" N LYS R 195 " --> pdb=" O ILE R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 252 removed outlier: 4.088A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 294 Proline residue: R 281 - end of helix removed outlier: 3.919A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 331 removed outlier: 3.809A pdb=" N LYS R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE R 304 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.641A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 342 196 hydrogen bonds defined for protein. 588 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: 0.61 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 623 1.33 - 1.45: 447 1.45 - 1.58: 1417 1.58 - 1.71: 2 1.71 - 1.83: 34 Bond restraints: 2523 Sorted by residual: bond pdb=" C ALA R 265 " pdb=" O ALA R 265 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.17e-02 7.31e+03 1.61e+01 bond pdb=" N ILE R 82 " pdb=" CA ILE R 82 " ideal model delta sigma weight residual 1.459 1.491 -0.033 9.10e-03 1.21e+04 1.28e+01 bond pdb=" C ILE R 270 " pdb=" O ILE R 270 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.13e-02 7.83e+03 1.23e+01 bond pdb=" CA ALA R 265 " pdb=" CB ALA R 265 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" N LEU R 103 " pdb=" CA LEU R 103 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 ... (remaining 2518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 3148 2.12 - 4.25: 248 4.25 - 6.37: 9 6.37 - 8.49: 1 8.49 - 10.61: 1 Bond angle restraints: 3407 Sorted by residual: angle pdb=" O GLN R 161 " pdb=" C GLN R 161 " pdb=" N GLN R 162 " ideal model delta sigma weight residual 121.76 126.04 -4.28 1.15e+00 7.56e-01 1.39e+01 angle pdb=" N GLU R 303 " pdb=" CA GLU R 303 " pdb=" CB GLU R 303 " ideal model delta sigma weight residual 110.16 115.17 -5.01 1.48e+00 4.57e-01 1.14e+01 angle pdb=" CD LYS R 254 " pdb=" CE LYS R 254 " pdb=" NZ LYS R 254 " ideal model delta sigma weight residual 111.90 101.29 10.61 3.20e+00 9.77e-02 1.10e+01 angle pdb=" CG LYS R 254 " pdb=" CD LYS R 254 " pdb=" CE LYS R 254 " ideal model delta sigma weight residual 111.30 118.44 -7.14 2.30e+00 1.89e-01 9.63e+00 angle pdb=" N ILE R 166 " pdb=" CA ILE R 166 " pdb=" C ILE R 166 " ideal model delta sigma weight residual 112.17 109.26 2.91 9.50e-01 1.11e+00 9.39e+00 ... (remaining 3402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 1414 24.76 - 49.51: 83 49.51 - 74.27: 8 74.27 - 99.02: 6 99.02 - 123.78: 3 Dihedral angle restraints: 1514 sinusoidal: 632 harmonic: 882 Sorted by residual: dihedral pdb=" O2 KW3 R 401 " pdb=" C4 KW3 R 401 " pdb=" C5 KW3 R 401 " pdb=" O6 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 296.46 172.68 123.78 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" N1 KW3 R 401 " pdb=" C28 KW3 R 401 " pdb=" C29 KW3 R 401 " pdb=" O9 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 57.01 -55.00 112.01 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1 KW3 R 401 " pdb=" C2 KW3 R 401 " pdb=" O1 KW3 R 401 " pdb=" C3 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 71.30 -178.59 -110.11 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 1511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 163 0.038 - 0.075: 119 0.075 - 0.113: 66 0.113 - 0.150: 43 0.150 - 0.188: 10 Chirality restraints: 401 Sorted by residual: chirality pdb=" CA ILE R 148 " pdb=" N ILE R 148 " pdb=" C ILE R 148 " pdb=" CB ILE R 148 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ILE R 156 " pdb=" N ILE R 156 " pdb=" C ILE R 156 " pdb=" CB ILE R 156 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA ILE R 98 " pdb=" N ILE R 98 " pdb=" C ILE R 98 " pdb=" CB ILE R 98 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 398 not shown) Planarity restraints: 399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 269 " 0.039 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE R 269 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE R 269 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 269 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 269 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE R 269 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 269 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 238 " 0.032 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR R 238 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 238 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR R 238 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 238 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR R 238 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR R 238 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR R 238 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 279 " 0.024 2.00e-02 2.50e+03 2.21e-02 8.53e+00 pdb=" CG PHE R 279 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 279 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 279 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE R 279 " 0.009 2.00e-02 2.50e+03 ... (remaining 396 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 186 2.76 - 3.29: 2780 3.29 - 3.83: 3984 3.83 - 4.36: 4780 4.36 - 4.90: 8162 Nonbonded interactions: 19892 Sorted by model distance: nonbonded pdb=" OH TYR R 282 " pdb=" NH2 ARG R 286 " model vdw 2.221 3.120 nonbonded pdb=" O LYS R 155 " pdb=" OG SER R 159 " model vdw 2.232 3.040 nonbonded pdb=" OG SER R 54 " pdb=" O HIS R 114 " model vdw 2.239 3.040 nonbonded pdb=" OG SER R 331 " pdb=" OD1 ASN R 333 " model vdw 2.276 3.040 nonbonded pdb=" O VAL R 78 " pdb=" ND1 HIS R 83 " model vdw 2.339 3.120 ... (remaining 19887 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.900 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.013 0.056 2525 Z= 0.934 Angle : 1.206 10.611 3411 Z= 0.876 Chirality : 0.071 0.188 401 Planarity : 0.006 0.027 399 Dihedral : 16.804 123.776 938 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 1.92 (0.45), residues: 296 helix: 2.03 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.99 (0.66), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.006 TRP R 179 HIS 0.007 0.002 HIS R 206 PHE 0.053 0.007 PHE R 269 TYR 0.045 0.008 TYR R 238 ARG 0.012 0.002 ARG R 110 Details of bonding type rmsd hydrogen bonds : bond 0.10752 ( 196) hydrogen bonds : angle 4.74204 ( 588) SS BOND : bond 0.03479 ( 2) SS BOND : angle 1.31959 ( 4) covalent geometry : bond 0.01281 ( 2523) covalent geometry : angle 1.20601 ( 3407) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: R 247 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.6991 (tpp-160) REVERT: R 251 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6919 (ptt180) REVERT: R 303 GLU cc_start: 0.7252 (pm20) cc_final: 0.6944 (pt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1727 time to fit residues: 12.9415 Evaluate side-chains 48 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 0.0170 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** 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 = 0.4238 r_free = 0.4238 target = 0.209475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.174956 restraints weight = 2629.703| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.64 r_work: 0.3717 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2525 Z= 0.132 Angle : 0.526 5.261 3411 Z= 0.290 Chirality : 0.039 0.138 401 Planarity : 0.003 0.026 399 Dihedral : 15.956 125.969 363 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.45 % Allowed : 11.27 % Favored : 87.27 % 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: 2.42 (0.47), residues: 296 helix: 2.42 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.10 (0.63), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.010 0.002 PHE R 134 TYR 0.011 0.001 TYR R 139 ARG 0.005 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 196) hydrogen bonds : angle 3.87533 ( 588) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.48025 ( 4) covalent geometry : bond 0.00256 ( 2523) covalent geometry : angle 0.52597 ( 3407) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.294 Fit side-chains REVERT: R 51 LYS cc_start: 0.7256 (mppt) cc_final: 0.6786 (tttt) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.1690 time to fit residues: 12.5445 Evaluate side-chains 56 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** 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 = 0.4184 r_free = 0.4184 target = 0.204178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.168555 restraints weight = 2632.295| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.67 r_work: 0.3643 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2525 Z= 0.155 Angle : 0.559 6.222 3411 Z= 0.302 Chirality : 0.040 0.137 401 Planarity : 0.004 0.037 399 Dihedral : 15.693 125.262 363 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.82 % Allowed : 13.82 % Favored : 84.36 % 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: 1.89 (0.46), residues: 296 helix: 2.08 (0.32), residues: 233 sheet: None (None), residues: 0 loop : -2.05 (0.60), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 228 HIS 0.004 0.001 HIS R 306 PHE 0.017 0.002 PHE R 227 TYR 0.016 0.002 TYR R 282 ARG 0.007 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 196) hydrogen bonds : angle 3.86838 ( 588) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.51986 ( 4) covalent geometry : bond 0.00334 ( 2523) covalent geometry : angle 0.55907 ( 3407) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.287 Fit side-chains REVERT: R 318 PHE cc_start: 0.7467 (t80) cc_final: 0.7156 (t80) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.1721 time to fit residues: 12.4759 Evaluate side-chains 60 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** 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 = 0.4202 r_free = 0.4202 target = 0.206044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170790 restraints weight = 2656.346| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.67 r_work: 0.3686 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2525 Z= 0.122 Angle : 0.492 5.028 3411 Z= 0.271 Chirality : 0.039 0.129 401 Planarity : 0.003 0.025 399 Dihedral : 15.860 128.475 363 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.00 % Allowed : 14.18 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.07 (0.47), residues: 296 helix: 2.22 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -2.04 (0.60), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.011 0.001 PHE R 227 TYR 0.012 0.001 TYR R 139 ARG 0.004 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 196) hydrogen bonds : angle 3.81406 ( 588) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.39642 ( 4) covalent geometry : bond 0.00232 ( 2523) covalent geometry : angle 0.49231 ( 3407) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.259 Fit side-chains REVERT: R 109 PHE cc_start: 0.6624 (m-80) cc_final: 0.6346 (m-80) REVERT: R 167 THR cc_start: 0.5897 (OUTLIER) cc_final: 0.5697 (p) REVERT: R 272 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7752 (tp) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.1593 time to fit residues: 12.2285 Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN ** R 206 HIS ** 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 = 0.4161 r_free = 0.4161 target = 0.201898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.169385 restraints weight = 2663.673| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.61 r_work: 0.3641 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2525 Z= 0.165 Angle : 0.564 5.324 3411 Z= 0.305 Chirality : 0.042 0.187 401 Planarity : 0.004 0.037 399 Dihedral : 16.095 125.876 363 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.64 % Allowed : 18.18 % Favored : 78.18 % 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: 1.55 (0.46), residues: 296 helix: 1.80 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -2.07 (0.61), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 228 HIS 0.005 0.001 HIS R 306 PHE 0.018 0.002 PHE R 227 TYR 0.018 0.002 TYR R 282 ARG 0.006 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 196) hydrogen bonds : angle 3.88808 ( 588) SS BOND : bond 0.00367 ( 2) SS BOND : angle 0.61566 ( 4) covalent geometry : bond 0.00356 ( 2523) covalent geometry : angle 0.56427 ( 3407) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.288 Fit side-chains REVERT: R 318 PHE cc_start: 0.7897 (t80) cc_final: 0.7590 (t80) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.1562 time to fit residues: 11.5825 Evaluate side-chains 58 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** R 206 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.203196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.170821 restraints weight = 2619.570| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.53 r_work: 0.3671 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2525 Z= 0.130 Angle : 0.514 5.054 3411 Z= 0.283 Chirality : 0.040 0.126 401 Planarity : 0.003 0.022 399 Dihedral : 15.836 126.428 363 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.00 % Allowed : 18.18 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.47), residues: 296 helix: 1.95 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.93 (0.62), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 PHE 0.012 0.001 PHE R 227 TYR 0.015 0.001 TYR R 282 ARG 0.003 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 196) hydrogen bonds : angle 3.88583 ( 588) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.60533 ( 4) covalent geometry : bond 0.00261 ( 2523) covalent geometry : angle 0.51371 ( 3407) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: R 80 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5213 (mt) REVERT: R 272 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8246 (tp) REVERT: R 315 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8099 (tt) REVERT: R 318 PHE cc_start: 0.7637 (t80) cc_final: 0.7327 (t80) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1590 time to fit residues: 11.9511 Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** 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 = 0.4250 r_free = 0.4250 target = 0.210538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.179147 restraints weight = 2676.739| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.49 r_work: 0.3721 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2525 Z= 0.122 Angle : 0.507 5.175 3411 Z= 0.278 Chirality : 0.039 0.139 401 Planarity : 0.003 0.022 399 Dihedral : 15.486 123.795 363 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.64 % Allowed : 19.64 % Favored : 76.73 % 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: 1.89 (0.47), residues: 296 helix: 2.04 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.87 (0.63), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 PHE 0.011 0.001 PHE R 227 TYR 0.019 0.001 TYR R 282 ARG 0.003 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 196) hydrogen bonds : angle 3.91286 ( 588) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.37787 ( 4) covalent geometry : bond 0.00238 ( 2523) covalent geometry : angle 0.50712 ( 3407) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.251 Fit side-chains REVERT: R 80 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.5009 (mt) REVERT: R 109 PHE cc_start: 0.6776 (m-80) cc_final: 0.6514 (m-80) REVERT: R 120 TRP cc_start: 0.7023 (t-100) cc_final: 0.6677 (t-100) REVERT: R 272 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8079 (tp) REVERT: R 315 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8032 (tt) REVERT: R 318 PHE cc_start: 0.7556 (t80) cc_final: 0.7222 (t80) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.1487 time to fit residues: 11.2532 Evaluate side-chains 63 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** 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 = 0.4160 r_free = 0.4160 target = 0.201640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.169091 restraints weight = 2669.535| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.62 r_work: 0.3641 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2525 Z= 0.165 Angle : 0.581 5.566 3411 Z= 0.311 Chirality : 0.042 0.138 401 Planarity : 0.004 0.034 399 Dihedral : 15.993 122.607 363 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.64 % Allowed : 21.09 % Favored : 75.27 % 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: 1.53 (0.47), residues: 296 helix: 1.73 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -1.81 (0.66), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 228 HIS 0.005 0.001 HIS R 306 PHE 0.018 0.002 PHE R 227 TYR 0.019 0.002 TYR R 282 ARG 0.004 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.05060 ( 196) hydrogen bonds : angle 4.01555 ( 588) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.62484 ( 4) covalent geometry : bond 0.00370 ( 2523) covalent geometry : angle 0.58061 ( 3407) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: R 80 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5669 (mt) REVERT: R 318 PHE cc_start: 0.7890 (t80) cc_final: 0.7558 (t80) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 0.1502 time to fit residues: 10.6892 Evaluate side-chains 62 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** 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 = 0.4161 r_free = 0.4161 target = 0.201588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.170443 restraints weight = 2646.288| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.47 r_work: 0.3651 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2525 Z= 0.166 Angle : 0.575 5.258 3411 Z= 0.313 Chirality : 0.042 0.160 401 Planarity : 0.004 0.026 399 Dihedral : 15.973 123.065 363 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.91 % Allowed : 20.73 % Favored : 76.36 % 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: 1.35 (0.46), residues: 296 helix: 1.57 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -1.73 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 228 HIS 0.003 0.001 HIS R 306 PHE 0.017 0.002 PHE R 227 TYR 0.020 0.002 TYR R 282 ARG 0.004 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 196) hydrogen bonds : angle 4.06700 ( 588) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.60966 ( 4) covalent geometry : bond 0.00374 ( 2523) covalent geometry : angle 0.57515 ( 3407) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: R 318 PHE cc_start: 0.7902 (t80) cc_final: 0.7568 (t80) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.1629 time to fit residues: 11.4226 Evaluate side-chains 62 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** 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 = 0.4168 r_free = 0.4168 target = 0.202455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.170480 restraints weight = 2666.606| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.62 r_work: 0.3671 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2525 Z= 0.134 Angle : 0.542 5.123 3411 Z= 0.299 Chirality : 0.041 0.158 401 Planarity : 0.003 0.022 399 Dihedral : 15.718 123.355 363 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.18 % Allowed : 20.73 % Favored : 77.09 % 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: 1.58 (0.46), residues: 296 helix: 1.77 (0.32), residues: 233 sheet: None (None), residues: 0 loop : -1.73 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 PHE 0.012 0.001 PHE R 227 TYR 0.020 0.001 TYR R 282 ARG 0.003 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 196) hydrogen bonds : angle 4.01557 ( 588) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.64166 ( 4) covalent geometry : bond 0.00277 ( 2523) covalent geometry : angle 0.54187 ( 3407) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.277 Fit side-chains REVERT: R 318 PHE cc_start: 0.7659 (t80) cc_final: 0.7352 (t80) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.1587 time to fit residues: 11.3358 Evaluate side-chains 65 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** 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 = 0.4148 r_free = 0.4148 target = 0.200215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.167850 restraints weight = 2713.818| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.60 r_work: 0.3650 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2525 Z= 0.156 Angle : 0.563 5.121 3411 Z= 0.309 Chirality : 0.042 0.175 401 Planarity : 0.004 0.028 399 Dihedral : 15.852 121.429 363 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.55 % Allowed : 20.00 % Favored : 77.45 % 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: 1.32 (0.46), residues: 296 helix: 1.59 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -1.91 (0.67), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 120 HIS 0.004 0.001 HIS R 306 PHE 0.015 0.002 PHE R 227 TYR 0.020 0.002 TYR R 282 ARG 0.004 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 196) hydrogen bonds : angle 4.04473 ( 588) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.80184 ( 4) covalent geometry : bond 0.00343 ( 2523) covalent geometry : angle 0.56272 ( 3407) =============================================================================== Job complete usr+sys time: 1685.27 seconds wall clock time: 29 minutes 47.18 seconds (1787.18 seconds total)