Starting phenix.real_space_refine on Fri May 9 19:34:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt7_18645/05_2025/8qt7_18645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt7_18645/05_2025/8qt7_18645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qt7_18645/05_2025/8qt7_18645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt7_18645/05_2025/8qt7_18645.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt7_18645/05_2025/8qt7_18645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt7_18645/05_2025/8qt7_18645.cif" } resolution = 2.2 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= 0.082 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 5 5.49 5 S 11 5.16 5 C 2282 2.51 5 N 555 2.21 5 O 661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3264 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 252 Unusual residues: {'FAD': 1, 'HEM': 2, 'NDP': 1} Classifications: {'undetermined': 4, 'water': 65} Link IDs: {None: 68} Time building chain proxies: 3.27, per 1000 atoms: 0.93 Number of scatterers: 3516 At special positions: 0 Unit cell: (59.592, 67.8432, 92.5968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 11 16.00 P 5 15.00 O 661 8.00 N 555 7.00 C 2282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 386.8 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 56.1% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.501A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 147 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.535A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.638A pdb=" N ALA A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 195 removed outlier: 8.084A pdb=" N TYR A 186 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY A 188 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A 208 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLN A 243 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR A 246 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 248 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER A 236 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N LYS A 250 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 220 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARG A 273 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LYS A 222 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU A 271 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 224 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL A 269 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.726A pdb=" N GLN A 287 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TYR A 316 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP A 289 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER A 318 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 291 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 391 " --> pdb=" O ALA A 365 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 555 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: 1.03 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 1513 1.39 - 1.57: 2020 1.57 - 1.75: 8 1.75 - 1.93: 22 1.93 - 2.12: 7 Bond restraints: 3570 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.599 0.234 3.80e-02 6.93e+02 3.78e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.590 0.167 3.50e-02 8.16e+02 2.29e+01 bond pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " ideal model delta sigma weight residual 1.544 1.458 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" O2N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.513 1.475 0.038 1.00e-02 1.00e+04 1.41e+01 ... (remaining 3565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 4857 5.53 - 11.05: 21 11.05 - 16.58: 1 16.58 - 22.10: 1 22.10 - 27.63: 1 Bond angle restraints: 4881 Sorted by residual: angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 135.37 -27.63 1.95e+00 2.62e-01 2.00e+02 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 121.33 -17.49 1.91e+00 2.73e-01 8.34e+01 angle pdb=" C5D NDP A 501 " pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 104.93 120.33 -15.40 2.66e+00 1.41e-01 3.35e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 111.64 5.82 1.17e+00 7.36e-01 2.50e+01 angle pdb=" O3 NDP A 501 " pdb=" PA NDP A 501 " pdb=" O5B NDP A 501 " ideal model delta sigma weight residual 108.94 98.09 10.85 2.49e+00 1.62e-01 1.90e+01 ... (remaining 4876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 1740 20.28 - 40.57: 199 40.57 - 60.85: 58 60.85 - 81.13: 8 81.13 - 101.42: 7 Dihedral angle restraints: 2012 sinusoidal: 850 harmonic: 1162 Sorted by residual: dihedral pdb=" C2B HEM A 503 " pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " pdb=" CBB HEM A 503 " ideal model delta sinusoidal sigma weight residual -0.00 49.42 -49.42 2 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 -83.54 -101.42 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" C1A HEM A 504 " pdb=" C2A HEM A 504 " pdb=" CAA HEM A 504 " pdb=" CBA HEM A 504 " ideal model delta sinusoidal sigma weight residual 180.00 94.44 85.56 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 2009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 416 0.053 - 0.106: 74 0.106 - 0.158: 17 0.158 - 0.211: 1 0.211 - 0.264: 1 Chirality restraints: 509 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.50 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 506 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.013 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C5N NDP A 501 " 0.027 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.028 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM A 503 " -0.010 2.00e-02 2.50e+03 1.33e-02 3.98e+00 pdb=" C2A HEM A 503 " -0.014 2.00e-02 2.50e+03 pdb=" C3A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" C4A HEM A 503 " -0.000 2.00e-02 2.50e+03 pdb=" CAA HEM A 503 " 0.003 2.00e-02 2.50e+03 pdb=" CHA HEM A 503 " 0.024 2.00e-02 2.50e+03 pdb=" CHB HEM A 503 " 0.015 2.00e-02 2.50e+03 pdb=" CMA HEM A 503 " 0.003 2.00e-02 2.50e+03 pdb=" NA HEM A 503 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A 503 " 0.008 2.00e-02 2.50e+03 1.01e-02 2.28e+00 pdb=" C1B HEM A 503 " 0.012 2.00e-02 2.50e+03 pdb=" C2B HEM A 503 " 0.002 2.00e-02 2.50e+03 pdb=" C3B HEM A 503 " 0.013 2.00e-02 2.50e+03 pdb=" C4B HEM A 503 " 0.006 2.00e-02 2.50e+03 pdb=" CAB HEM A 503 " -0.005 2.00e-02 2.50e+03 pdb=" CHB HEM A 503 " -0.014 2.00e-02 2.50e+03 pdb=" CHC HEM A 503 " -0.015 2.00e-02 2.50e+03 pdb=" CMB HEM A 503 " -0.006 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 141 2.72 - 3.26: 3343 3.26 - 3.81: 6373 3.81 - 4.35: 8207 4.35 - 4.90: 13086 Nonbonded interactions: 31150 Sorted by model distance: nonbonded pdb=" NE2 HIS A 69 " pdb="FE HEM A 504 " model vdw 2.169 3.080 nonbonded pdb=" NE2 HIS A 142 " pdb="FE HEM A 503 " model vdw 2.174 3.080 nonbonded pdb=" O1P FAD A 502 " pdb=" O HOH A 601 " model vdw 2.214 3.040 nonbonded pdb=" CG2 THR A 28 " pdb=" O HOH A 662 " model vdw 2.230 3.460 nonbonded pdb=" OE1 GLU A 229 " pdb=" O HOH A 602 " model vdw 2.232 3.040 ... (remaining 31145 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: 0.010 Normalize map: mean=0, sd=1: 1.120 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.009 0.234 3572 Z= 0.361 Angle : 0.959 27.630 4881 Z= 0.431 Chirality : 0.045 0.264 509 Planarity : 0.003 0.021 581 Dihedral : 19.299 101.415 1272 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.86 % Allowed : 19.31 % Favored : 79.83 % 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: 1.00 (0.42), residues: 397 helix: 1.33 (0.37), residues: 193 sheet: 0.26 (0.52), residues: 96 loop : 0.05 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 127 HIS 0.006 0.001 HIS A 142 PHE 0.010 0.001 PHE A 218 TYR 0.011 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.14620 ( 193) hydrogen bonds : angle 6.89758 ( 555) covalent geometry : bond 0.00930 ( 3570) covalent geometry : angle 0.95881 ( 4881) Misc. bond : bond 0.03082 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.378 Fit side-chains REVERT: A 226 GLU cc_start: 0.7138 (tt0) cc_final: 0.6912 (mp0) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.9884 time to fit residues: 52.4446 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 160 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.128424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109096 restraints weight = 3276.114| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.25 r_work: 0.3147 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.232 3572 Z= 0.147 Angle : 0.636 14.209 4881 Z= 0.282 Chirality : 0.042 0.139 509 Planarity : 0.003 0.022 581 Dihedral : 12.659 107.693 513 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.88 % Allowed : 17.00 % Favored : 80.12 % 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: 1.67 (0.43), residues: 397 helix: 2.18 (0.36), residues: 196 sheet: 0.29 (0.52), residues: 96 loop : -0.05 (0.64), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.012 0.001 PHE A 218 TYR 0.012 0.002 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 193) hydrogen bonds : angle 4.80241 ( 555) covalent geometry : bond 0.00331 ( 3570) covalent geometry : angle 0.63626 ( 4881) Misc. bond : bond 0.22010 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.323 Fit side-chains REVERT: A 226 GLU cc_start: 0.7769 (tt0) cc_final: 0.7077 (mp0) REVERT: A 323 GLU cc_start: 0.6799 (pm20) cc_final: 0.6323 (pm20) REVERT: A 385 LYS cc_start: 0.7150 (tmmt) cc_final: 0.6391 (tttp) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.9844 time to fit residues: 59.3347 Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 0.0070 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.129757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110464 restraints weight = 3329.197| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.26 r_work: 0.3163 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 3572 Z= 0.123 Angle : 0.590 13.421 4881 Z= 0.258 Chirality : 0.040 0.137 509 Planarity : 0.003 0.021 581 Dihedral : 12.242 106.842 512 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.31 % Allowed : 17.29 % Favored : 80.40 % 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: 1.72 (0.43), residues: 397 helix: 2.27 (0.36), residues: 196 sheet: 0.28 (0.53), residues: 95 loop : -0.12 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.006 0.001 HIS A 142 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 193) hydrogen bonds : angle 4.58878 ( 555) covalent geometry : bond 0.00272 ( 3570) covalent geometry : angle 0.58971 ( 4881) Misc. bond : bond 0.20139 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.383 Fit side-chains REVERT: A 226 GLU cc_start: 0.7796 (tt0) cc_final: 0.7084 (mp0) REVERT: A 385 LYS cc_start: 0.7070 (tmmt) cc_final: 0.6300 (tttp) outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 1.0152 time to fit residues: 63.3447 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.129037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110189 restraints weight = 3308.493| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.23 r_work: 0.3165 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 3572 Z= 0.126 Angle : 0.602 13.683 4881 Z= 0.261 Chirality : 0.040 0.140 509 Planarity : 0.003 0.021 581 Dihedral : 12.226 107.678 511 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.31 % Allowed : 17.58 % Favored : 80.12 % 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: 1.70 (0.43), residues: 397 helix: 2.30 (0.36), residues: 196 sheet: 0.22 (0.53), residues: 95 loop : -0.14 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 193) hydrogen bonds : angle 4.58556 ( 555) covalent geometry : bond 0.00279 ( 3570) covalent geometry : angle 0.60203 ( 4881) Misc. bond : bond 0.20016 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.388 Fit side-chains REVERT: A 226 GLU cc_start: 0.7787 (tt0) cc_final: 0.7094 (mp0) REVERT: A 385 LYS cc_start: 0.7203 (tmmt) cc_final: 0.6566 (tmmt) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 1.0111 time to fit residues: 61.8995 Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.128269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108836 restraints weight = 3340.448| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.27 r_work: 0.3139 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.218 3572 Z= 0.155 Angle : 0.646 14.295 4881 Z= 0.283 Chirality : 0.042 0.141 509 Planarity : 0.003 0.022 581 Dihedral : 12.495 110.144 511 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % Favored : 80.12 % 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: 1.58 (0.43), residues: 397 helix: 2.16 (0.36), residues: 196 sheet: 0.21 (0.53), residues: 95 loop : -0.17 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.008 0.001 HIS A 142 PHE 0.013 0.001 PHE A 218 TYR 0.010 0.002 TYR A 275 ARG 0.001 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 193) hydrogen bonds : angle 4.73365 ( 555) covalent geometry : bond 0.00348 ( 3570) covalent geometry : angle 0.64617 ( 4881) Misc. bond : bond 0.21057 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.383 Fit side-chains REVERT: A 226 GLU cc_start: 0.7813 (tt0) cc_final: 0.7097 (mp0) REVERT: A 285 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6830 (tt0) REVERT: A 323 GLU cc_start: 0.6764 (pm20) cc_final: 0.6399 (pm20) REVERT: A 385 LYS cc_start: 0.7312 (tmmt) cc_final: 0.6580 (tmmt) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.9690 time to fit residues: 54.4031 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 0.5170 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.131024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111715 restraints weight = 3368.110| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.27 r_work: 0.3181 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 3572 Z= 0.110 Angle : 0.565 12.625 4881 Z= 0.249 Chirality : 0.039 0.141 509 Planarity : 0.003 0.021 581 Dihedral : 12.073 108.767 511 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.44 % Allowed : 18.44 % Favored : 80.12 % 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: 1.75 (0.43), residues: 397 helix: 2.38 (0.36), residues: 196 sheet: 0.21 (0.53), residues: 95 loop : -0.19 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.005 0.001 HIS A 142 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 193) hydrogen bonds : angle 4.47202 ( 555) covalent geometry : bond 0.00243 ( 3570) covalent geometry : angle 0.56526 ( 4881) Misc. bond : bond 0.19029 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.389 Fit side-chains REVERT: A 226 GLU cc_start: 0.7788 (tt0) cc_final: 0.7083 (mp0) REVERT: A 285 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: A 385 LYS cc_start: 0.7232 (tmmt) cc_final: 0.6492 (tmmt) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 1.0533 time to fit residues: 60.1234 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.128185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108931 restraints weight = 3310.732| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.25 r_work: 0.3144 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.212 3572 Z= 0.156 Angle : 0.642 14.108 4881 Z= 0.283 Chirality : 0.042 0.141 509 Planarity : 0.003 0.022 581 Dihedral : 12.490 113.317 511 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.44 % Allowed : 18.44 % Favored : 80.12 % 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: 1.61 (0.43), residues: 397 helix: 2.15 (0.36), residues: 197 sheet: 0.22 (0.53), residues: 95 loop : -0.10 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.008 0.001 HIS A 142 PHE 0.013 0.001 PHE A 218 TYR 0.010 0.002 TYR A 275 ARG 0.001 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 193) hydrogen bonds : angle 4.69916 ( 555) covalent geometry : bond 0.00352 ( 3570) covalent geometry : angle 0.64212 ( 4881) Misc. bond : bond 0.20582 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.351 Fit side-chains REVERT: A 226 GLU cc_start: 0.7817 (tt0) cc_final: 0.7104 (mp0) REVERT: A 285 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: A 385 LYS cc_start: 0.7333 (tmmt) cc_final: 0.6590 (tmmt) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.9268 time to fit residues: 51.1573 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.129726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110441 restraints weight = 3331.657| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.26 r_work: 0.3161 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.205 3572 Z= 0.129 Angle : 0.602 13.477 4881 Z= 0.264 Chirality : 0.041 0.142 509 Planarity : 0.003 0.022 581 Dihedral : 12.345 113.955 511 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 17.87 % Favored : 80.40 % 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: 1.66 (0.43), residues: 397 helix: 2.23 (0.36), residues: 197 sheet: 0.21 (0.53), residues: 95 loop : -0.14 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.011 0.001 PHE A 218 TYR 0.011 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 193) hydrogen bonds : angle 4.59141 ( 555) covalent geometry : bond 0.00288 ( 3570) covalent geometry : angle 0.60242 ( 4881) Misc. bond : bond 0.20366 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.359 Fit side-chains REVERT: A 226 GLU cc_start: 0.7800 (tt0) cc_final: 0.7088 (mp0) REVERT: A 385 LYS cc_start: 0.7273 (tmmt) cc_final: 0.6527 (tmmt) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.8698 time to fit residues: 49.9108 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111512 restraints weight = 3244.812| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.25 r_work: 0.3176 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 3572 Z= 0.118 Angle : 0.588 12.979 4881 Z= 0.260 Chirality : 0.041 0.142 509 Planarity : 0.003 0.022 581 Dihedral : 12.186 113.372 511 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.86 % Allowed : 18.73 % Favored : 80.40 % 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: 1.73 (0.43), residues: 397 helix: 2.32 (0.36), residues: 197 sheet: 0.21 (0.53), residues: 95 loop : -0.13 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.006 0.001 HIS A 142 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 193) hydrogen bonds : angle 4.53840 ( 555) covalent geometry : bond 0.00264 ( 3570) covalent geometry : angle 0.58764 ( 4881) Misc. bond : bond 0.19516 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.398 Fit side-chains REVERT: A 226 GLU cc_start: 0.7794 (tt0) cc_final: 0.7094 (mp0) REVERT: A 385 LYS cc_start: 0.7202 (tmmt) cc_final: 0.6474 (tmmt) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.9792 time to fit residues: 55.0218 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.131381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112099 restraints weight = 3293.248| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.26 r_work: 0.3182 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 3572 Z= 0.116 Angle : 0.587 13.007 4881 Z= 0.260 Chirality : 0.040 0.142 509 Planarity : 0.003 0.021 581 Dihedral : 12.126 112.765 511 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.15 % Allowed : 18.73 % Favored : 80.12 % 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: 1.75 (0.43), residues: 397 helix: 2.35 (0.36), residues: 197 sheet: 0.20 (0.53), residues: 95 loop : -0.14 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.006 0.001 HIS A 142 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 193) hydrogen bonds : angle 4.51105 ( 555) covalent geometry : bond 0.00259 ( 3570) covalent geometry : angle 0.58695 ( 4881) Misc. bond : bond 0.19109 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.348 Fit side-chains REVERT: A 226 GLU cc_start: 0.7794 (tt0) cc_final: 0.7089 (mp0) REVERT: A 323 GLU cc_start: 0.6513 (pm20) cc_final: 0.6221 (pm20) REVERT: A 385 LYS cc_start: 0.7161 (tmmt) cc_final: 0.6453 (tmmt) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.9625 time to fit residues: 55.0181 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.126817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107493 restraints weight = 3323.309| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.25 r_work: 0.3121 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 3572 Z= 0.211 Angle : 0.710 13.990 4881 Z= 0.321 Chirality : 0.046 0.141 509 Planarity : 0.004 0.024 581 Dihedral : 13.068 122.330 511 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.86 % Allowed : 19.02 % Favored : 80.12 % 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: 1.34 (0.42), residues: 397 helix: 1.74 (0.36), residues: 203 sheet: 0.16 (0.53), residues: 95 loop : 0.00 (0.65), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 125 HIS 0.010 0.002 HIS A 142 PHE 0.016 0.002 PHE A 218 TYR 0.013 0.002 TYR A 66 ARG 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 193) hydrogen bonds : angle 4.92388 ( 555) covalent geometry : bond 0.00489 ( 3570) covalent geometry : angle 0.70972 ( 4881) Misc. bond : bond 0.21737 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.93 seconds wall clock time: 54 minutes 34.07 seconds (3274.07 seconds total)