Starting phenix.real_space_refine on Fri Feb 14 13:50:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ds6_27684/02_2025/8ds6_27684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ds6_27684/02_2025/8ds6_27684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ds6_27684/02_2025/8ds6_27684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ds6_27684/02_2025/8ds6_27684.map" model { file = "/net/cci-nas-00/data/ceres_data/8ds6_27684/02_2025/8ds6_27684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ds6_27684/02_2025/8ds6_27684.cif" } resolution = 4.9 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= 0.001 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 S 20 5.16 5 C 3224 2.51 5 N 909 2.21 5 O 875 1.98 5 H 5107 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10135 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5051 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 34, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5084 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 35, 'TRANS': 299} Chain breaks: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.53 Number of scatterers: 10135 At special positions: 0 Unit cell: (72.645, 101.87, 108.55, 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 20 16.00 O 875 8.00 N 909 7.00 C 3224 6.00 H 5107 1.00 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=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 748.5 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 52.6% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 130 through 158 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.812A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 299 removed outlier: 3.507A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 348 through 361 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 387 through 400 Processing helix chain 'A' and resid 420 through 440 Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.528A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 214 through 224 removed outlier: 4.115A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.758A pdb=" N GLU B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 298 removed outlier: 3.603A pdb=" N VAL B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 368 through 385 removed outlier: 3.515A pdb=" N ALA B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 415 through 418 Processing helix chain 'B' and resid 419 through 441 Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 460 through 472 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 173 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.652A pdb=" N ALA A 252 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 235 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 173 removed outlier: 3.614A pdb=" N ALA B 180 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 173 removed outlier: 5.096A pdb=" N ALA B 252 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY B 235 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 302 318 hydrogen bonds defined for protein. 909 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: 3.57 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.09: 4677 1.09 - 1.27: 1221 1.27 - 1.45: 1392 1.45 - 1.63: 2965 1.63 - 1.81: 24 Bond restraints: 10279 Sorted by residual: bond pdb=" CD2 PHE B 294 " pdb=" HD2 PHE B 294 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" CD2 HIS B 348 " pdb=" HD2 HIS B 348 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" CD2 HIS A 227 " pdb=" HD2 HIS A 227 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" CZ2 TRP A 450 " pdb=" HZ2 TRP A 450 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" CZ3 TRP A 400 " pdb=" HZ3 TRP A 400 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.48e+01 ... (remaining 10274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 16165 2.61 - 5.21: 1903 5.21 - 7.82: 620 7.82 - 10.43: 16 10.43 - 13.04: 17 Bond angle restraints: 18721 Sorted by residual: angle pdb=" N ALA A 291 " pdb=" CA ALA A 291 " pdb=" C ALA A 291 " ideal model delta sigma weight residual 111.28 103.64 7.64 1.09e+00 8.42e-01 4.91e+01 angle pdb=" N PRO B 338 " pdb=" CA PRO B 338 " pdb=" C PRO B 338 " ideal model delta sigma weight residual 110.70 119.16 -8.46 1.22e+00 6.72e-01 4.81e+01 angle pdb=" C GLY A 322 " pdb=" N PRO A 323 " pdb=" CA PRO A 323 " ideal model delta sigma weight residual 119.66 124.05 -4.39 7.20e-01 1.93e+00 3.72e+01 angle pdb=" CA PRO B 338 " pdb=" C PRO B 338 " pdb=" N PRO B 339 " ideal model delta sigma weight residual 117.93 124.66 -6.73 1.20e+00 6.94e-01 3.14e+01 angle pdb=" CA GLU B 132 " pdb=" C GLU B 132 " pdb=" O GLU B 132 " ideal model delta sigma weight residual 120.55 114.88 5.67 1.06e+00 8.90e-01 2.86e+01 ... (remaining 18716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4554 17.82 - 35.63: 156 35.63 - 53.45: 106 53.45 - 71.26: 34 71.26 - 89.08: 4 Dihedral angle restraints: 4854 sinusoidal: 2698 harmonic: 2156 Sorted by residual: dihedral pdb=" CA PRO B 273 " pdb=" C PRO B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA THR B 329 " pdb=" C THR B 329 " pdb=" N ASP B 330 " pdb=" CA ASP B 330 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLY B 343 " pdb=" C GLY B 343 " pdb=" N SER B 344 " pdb=" CA SER B 344 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 514 0.051 - 0.102: 230 0.102 - 0.152: 33 0.152 - 0.203: 20 0.203 - 0.254: 2 Chirality restraints: 799 Sorted by residual: chirality pdb=" CA ASP A 473 " pdb=" N ASP A 473 " pdb=" C ASP A 473 " pdb=" CB ASP A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL A 237 " pdb=" N VAL A 237 " pdb=" C VAL A 237 " pdb=" CB VAL A 237 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL B 237 " pdb=" N VAL B 237 " pdb=" C VAL B 237 " pdb=" CB VAL B 237 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 796 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 325 " 0.298 9.50e-02 1.11e+02 1.22e-01 1.21e+02 pdb=" NE ARG B 325 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 325 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 325 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 325 " -0.062 2.00e-02 2.50e+03 pdb="HH11 ARG B 325 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 325 " -0.080 2.00e-02 2.50e+03 pdb="HH21 ARG B 325 " -0.084 2.00e-02 2.50e+03 pdb="HH22 ARG B 325 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 325 " -0.413 9.50e-02 1.11e+02 1.48e-01 8.69e+01 pdb=" NE ARG A 325 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A 325 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 325 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 325 " 0.049 2.00e-02 2.50e+03 pdb="HH11 ARG A 325 " 0.051 2.00e-02 2.50e+03 pdb="HH12 ARG A 325 " 0.018 2.00e-02 2.50e+03 pdb="HH21 ARG A 325 " 0.080 2.00e-02 2.50e+03 pdb="HH22 ARG A 325 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " 0.171 9.50e-02 1.11e+02 6.96e-02 3.91e+01 pdb=" NE ARG B 192 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " -0.033 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " 0.024 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " -0.049 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " -0.034 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " 0.092 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 995 2.24 - 2.83: 20752 2.83 - 3.42: 28654 3.42 - 4.01: 37970 4.01 - 4.60: 55049 Nonbonded interactions: 143420 Sorted by model distance: nonbonded pdb=" O TRP B 450 " pdb=" HG CYS B 453 " model vdw 1.650 2.620 nonbonded pdb=" O TRP A 450 " pdb=" HG CYS A 453 " model vdw 1.689 2.620 nonbonded pdb="HG23 THR A 368 " pdb=" H ALA A 371 " model vdw 1.707 2.270 nonbonded pdb=" HD2 ARG A 156 " pdb="HH11 ARG A 156 " model vdw 1.716 2.270 nonbonded pdb=" O LEU A 266 " pdb=" HG CYS A 270 " model vdw 1.728 2.620 ... (remaining 143415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 130 through 472) selection = (chain 'B' and (resid 130 through 406 or resid 419 through 472)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.180 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.670 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.012 0.075 5172 Z= 0.820 Angle : 1.434 8.458 7088 Z= 1.063 Chirality : 0.062 0.254 799 Planarity : 0.010 0.119 923 Dihedral : 10.651 89.081 1879 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 1.06 (0.30), residues: 661 helix: 1.33 (0.26), residues: 322 sheet: 0.06 (0.51), residues: 62 loop : 0.26 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 400 HIS 0.004 0.000 HIS A 135 PHE 0.014 0.001 PHE B 331 TYR 0.001 0.000 TYR A 188 ARG 0.007 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8081 (tpp80) REVERT: B 268 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8733 (mp0) REVERT: B 398 LEU cc_start: 0.8050 (mt) cc_final: 0.7797 (mt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.4617 time to fit residues: 50.7120 Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.050069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.038270 restraints weight = 119545.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.040093 restraints weight = 70517.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.041469 restraints weight = 47958.932| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5172 Z= 0.254 Angle : 0.621 6.036 7088 Z= 0.331 Chirality : 0.037 0.135 799 Planarity : 0.006 0.050 923 Dihedral : 4.338 16.391 722 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.80 (0.31), residues: 661 helix: 2.43 (0.27), residues: 326 sheet: -0.53 (0.49), residues: 84 loop : 0.24 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 216 HIS 0.003 0.001 HIS B 169 PHE 0.013 0.001 PHE A 331 TYR 0.008 0.001 TYR B 187 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.8460 (tp) cc_final: 0.8119 (tt) REVERT: B 247 TRP cc_start: 0.7636 (p90) cc_final: 0.6982 (p90) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.4811 time to fit residues: 43.8791 Evaluate side-chains 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.0030 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 overall best weight: 0.5448 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.051282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.038913 restraints weight = 119521.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.040867 restraints weight = 69291.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.042315 restraints weight = 46751.156| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5172 Z= 0.163 Angle : 0.541 5.688 7088 Z= 0.271 Chirality : 0.037 0.135 799 Planarity : 0.006 0.051 923 Dihedral : 3.976 14.397 722 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.32), residues: 661 helix: 2.65 (0.27), residues: 327 sheet: -0.75 (0.49), residues: 84 loop : 0.39 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 450 HIS 0.003 0.001 HIS A 161 PHE 0.011 0.001 PHE B 171 TYR 0.023 0.002 TYR B 455 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 464 MET cc_start: 0.7479 (mmm) cc_final: 0.7152 (mmp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3827 time to fit residues: 31.9978 Evaluate side-chains 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.049934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.038284 restraints weight = 125657.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.040106 restraints weight = 73882.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.041505 restraints weight = 49712.186| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5172 Z= 0.213 Angle : 0.551 5.739 7088 Z= 0.282 Chirality : 0.036 0.142 799 Planarity : 0.006 0.047 923 Dihedral : 3.962 14.633 722 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.84 (0.32), residues: 661 helix: 2.59 (0.28), residues: 326 sheet: -1.02 (0.48), residues: 78 loop : 0.24 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.005 0.001 HIS B 348 PHE 0.012 0.001 PHE A 331 TYR 0.010 0.002 TYR B 455 ARG 0.003 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLU cc_start: 0.9336 (mt-10) cc_final: 0.8983 (tm-30) REVERT: B 464 MET cc_start: 0.7385 (mmm) cc_final: 0.6911 (mmp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3799 time to fit residues: 29.9489 Evaluate side-chains 52 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.050221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.038560 restraints weight = 125867.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.040408 restraints weight = 73887.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.041824 restraints weight = 50036.135| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5172 Z= 0.143 Angle : 0.501 5.543 7088 Z= 0.248 Chirality : 0.036 0.136 799 Planarity : 0.006 0.048 923 Dihedral : 3.710 13.841 722 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.08 (0.33), residues: 661 helix: 2.85 (0.28), residues: 326 sheet: -1.10 (0.47), residues: 84 loop : 0.38 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.002 0.000 HIS B 135 PHE 0.010 0.001 PHE B 171 TYR 0.006 0.001 TYR A 188 ARG 0.001 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 TYR cc_start: 0.9016 (m-80) cc_final: 0.8454 (m-80) REVERT: B 219 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9060 (tm-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3652 time to fit residues: 29.2827 Evaluate side-chains 52 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.5764 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.049404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.038344 restraints weight = 129931.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.040073 restraints weight = 75897.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.041375 restraints weight = 51394.732| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5172 Z= 0.195 Angle : 0.527 5.656 7088 Z= 0.265 Chirality : 0.036 0.142 799 Planarity : 0.006 0.042 923 Dihedral : 3.701 13.498 722 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.99 (0.34), residues: 661 helix: 2.74 (0.28), residues: 326 sheet: -1.21 (0.48), residues: 78 loop : 0.36 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.004 0.001 HIS A 166 PHE 0.008 0.001 PHE A 294 TYR 0.008 0.001 TYR B 187 ARG 0.002 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8915 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3879 time to fit residues: 30.1208 Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN ** B 135 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 = 0.3537 r_free = 0.3537 target = 0.049983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.038626 restraints weight = 128192.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.040394 restraints weight = 74890.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.041745 restraints weight = 50835.744| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5172 Z= 0.136 Angle : 0.490 5.532 7088 Z= 0.241 Chirality : 0.036 0.138 799 Planarity : 0.005 0.044 923 Dihedral : 3.562 13.756 722 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.34), residues: 661 helix: 2.97 (0.28), residues: 326 sheet: -1.11 (0.48), residues: 84 loop : 0.46 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.005 0.001 HIS A 135 PHE 0.014 0.001 PHE B 171 TYR 0.006 0.001 TYR A 188 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 TYR cc_start: 0.8982 (m-80) cc_final: 0.8476 (m-80) REVERT: B 219 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9037 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3829 time to fit residues: 30.6855 Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.049948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.038678 restraints weight = 130821.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.040448 restraints weight = 78154.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.041783 restraints weight = 53181.274| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5172 Z= 0.141 Angle : 0.491 5.553 7088 Z= 0.240 Chirality : 0.036 0.138 799 Planarity : 0.005 0.043 923 Dihedral : 3.523 13.663 722 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.30 (0.34), residues: 661 helix: 3.06 (0.28), residues: 326 sheet: -1.09 (0.48), residues: 84 loop : 0.47 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.002 0.000 HIS A 166 PHE 0.006 0.001 PHE A 294 TYR 0.006 0.001 TYR A 188 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 TYR cc_start: 0.8975 (m-80) cc_final: 0.8429 (m-80) REVERT: B 219 GLU cc_start: 0.9473 (mt-10) cc_final: 0.9023 (tm-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3847 time to fit residues: 29.0400 Evaluate side-chains 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.049984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.038741 restraints weight = 132212.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.040504 restraints weight = 79472.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.041857 restraints weight = 54191.536| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5172 Z= 0.149 Angle : 0.496 5.495 7088 Z= 0.243 Chirality : 0.036 0.138 799 Planarity : 0.005 0.041 923 Dihedral : 3.467 13.154 722 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 2.28 (0.34), residues: 661 helix: 3.07 (0.28), residues: 325 sheet: -1.10 (0.48), residues: 84 loop : 0.44 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.002 0.001 HIS A 166 PHE 0.015 0.001 PHE B 171 TYR 0.006 0.001 TYR A 188 ARG 0.002 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9005 (tm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3363 time to fit residues: 25.0104 Evaluate side-chains 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 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 = 0.3523 r_free = 0.3523 target = 0.049773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.038505 restraints weight = 133243.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.040252 restraints weight = 80229.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.041616 restraints weight = 54891.878| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5172 Z= 0.167 Angle : 0.505 5.552 7088 Z= 0.250 Chirality : 0.036 0.138 799 Planarity : 0.005 0.036 923 Dihedral : 3.484 12.775 722 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 2.22 (0.34), residues: 661 helix: 3.03 (0.28), residues: 325 sheet: -1.13 (0.48), residues: 84 loop : 0.40 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 216 HIS 0.007 0.001 HIS A 135 PHE 0.007 0.001 PHE A 294 TYR 0.006 0.001 TYR A 188 ARG 0.002 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3404 time to fit residues: 23.9085 Evaluate side-chains 41 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.049713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.038536 restraints weight = 132465.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.040280 restraints weight = 80316.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.041597 restraints weight = 55162.037| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5172 Z= 0.182 Angle : 0.522 5.528 7088 Z= 0.259 Chirality : 0.036 0.138 799 Planarity : 0.006 0.073 923 Dihedral : 3.529 12.511 722 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.13 (0.34), residues: 661 helix: 2.93 (0.28), residues: 325 sheet: -1.27 (0.49), residues: 78 loop : 0.36 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 472 HIS 0.007 0.001 HIS B 169 PHE 0.036 0.002 PHE B 171 TYR 0.006 0.001 TYR A 188 ARG 0.007 0.000 ARG B 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.62 seconds wall clock time: 64 minutes 31.45 seconds (3871.45 seconds total)