Starting phenix.real_space_refine on Fri Dec 27 07:45:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwj_27756/12_2024/8dwj_27756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwj_27756/12_2024/8dwj_27756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwj_27756/12_2024/8dwj_27756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwj_27756/12_2024/8dwj_27756.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwj_27756/12_2024/8dwj_27756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwj_27756/12_2024/8dwj_27756.cif" } resolution = 3.9 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= 0.003 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 Zn 1 6.06 5 P 14 5.49 5 S 13 5.16 5 C 1905 2.51 5 N 525 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3043 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP P 1 " pdbres=" C P 2 " Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 24, 'TRANS': 314} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 556 SG CYS A 37 35.483 27.676 19.865 1.00234.26 S ATOM 576 SG CYS A 40 35.253 23.162 19.878 1.00251.45 S ATOM 775 SG CYS A 65 36.508 25.850 23.034 1.00220.03 S ATOM 801 SG CYS A 68 38.485 25.430 20.056 1.00211.90 S Time building chain proxies: 3.30, per 1000 atoms: 1.08 Number of scatterers: 3043 At special positions: 0 Unit cell: (67.914, 67.914, 82.32, 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) Zn 1 29.99 S 13 16.00 P 14 15.00 O 585 8.00 N 525 7.00 C 1905 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 502.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 65 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 68 " Number of angles added : 6 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 4 sheets defined 38.9% alpha, 14.2% beta 3 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 82 through 97 removed outlier: 3.545A pdb=" N ARG A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.212A pdb=" N LYS A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.522A pdb=" N ALA A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.512A pdb=" N ILE A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 4.306A pdb=" N LYS A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 116 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 801 1.34 - 1.45: 621 1.45 - 1.57: 1675 1.57 - 1.69: 25 1.69 - 1.81: 20 Bond restraints: 3142 Sorted by residual: bond pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.21e-02 6.83e+03 8.34e+00 bond pdb=" N ILE A 308 " pdb=" CA ILE A 308 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 8.01e+00 bond pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.83e+00 bond pdb=" N ILE A 103 " pdb=" CA ILE A 103 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.56e+00 bond pdb=" N SER A 100 " pdb=" CA SER A 100 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.40e+00 ... (remaining 3137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 4121 2.27 - 4.54: 141 4.54 - 6.80: 20 6.80 - 9.07: 9 9.07 - 11.34: 6 Bond angle restraints: 4297 Sorted by residual: angle pdb=" N ARG A 87 " pdb=" CA ARG A 87 " pdb=" C ARG A 87 " ideal model delta sigma weight residual 110.97 105.46 5.51 1.09e+00 8.42e-01 2.55e+01 angle pdb=" CA LYS A 161 " pdb=" CB LYS A 161 " pdb=" CG LYS A 161 " ideal model delta sigma weight residual 114.10 122.41 -8.31 2.00e+00 2.50e-01 1.73e+01 angle pdb=" PB GTP P 1 " pdb=" O3B GTP P 1 " pdb=" PG GTP P 1 " ideal model delta sigma weight residual 120.50 131.84 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " ideal model delta sigma weight residual 112.70 123.89 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C TYR A 86 " pdb=" N ARG A 87 " pdb=" CA ARG A 87 " ideal model delta sigma weight residual 120.65 115.88 4.77 1.32e+00 5.74e-01 1.30e+01 ... (remaining 4292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 1660 17.58 - 35.16: 166 35.16 - 52.73: 44 52.73 - 70.31: 16 70.31 - 87.88: 7 Dihedral angle restraints: 1893 sinusoidal: 895 harmonic: 998 Sorted by residual: dihedral pdb=" C5' GTP P 1 " pdb=" O5' GTP P 1 " pdb=" PA GTP P 1 " pdb=" O3A GTP P 1 " ideal model delta sinusoidal sigma weight residual 69.27 143.55 -74.28 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" C8 GTP P 1 " pdb=" C1' GTP P 1 " pdb=" N9 GTP P 1 " pdb=" O4' GTP P 1 " ideal model delta sinusoidal sigma weight residual 104.59 42.71 61.88 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CA GLU A 114 " pdb=" C GLU A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 1890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 274 0.040 - 0.079: 101 0.079 - 0.118: 44 0.118 - 0.158: 22 0.158 - 0.197: 10 Chirality restraints: 451 Sorted by residual: chirality pdb=" CA MET A 281 " pdb=" N MET A 281 " pdb=" C MET A 281 " pdb=" CB MET A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LEU A 336 " pdb=" N LEU A 336 " pdb=" C LEU A 336 " pdb=" CB LEU A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA MET A 307 " pdb=" N MET A 307 " pdb=" C MET A 307 " pdb=" CB MET A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 448 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 145 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 146 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 203 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.58e+00 pdb=" N PRO A 204 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 314 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 315 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.032 5.00e-02 4.00e+02 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 364 2.75 - 3.29: 2886 3.29 - 3.83: 5595 3.83 - 4.36: 6432 4.36 - 4.90: 10310 Nonbonded interactions: 25587 Sorted by model distance: nonbonded pdb=" OD1 ASP A 8 " pdb=" OH TYR A 89 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR A 55 " pdb=" OH TYR A 66 " model vdw 2.305 3.040 nonbonded pdb=" O LEU A 268 " pdb=" NE1 TRP A 294 " model vdw 2.370 3.120 nonbonded pdb=" NE2 GLN A 195 " pdb=" OG1 THR A 209 " model vdw 2.380 3.120 nonbonded pdb=" N ASP A 84 " pdb=" OD1 ASP A 84 " model vdw 2.384 3.120 ... (remaining 25582 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 ========== 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 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.770 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 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 : 0.005 0.049 3142 Z= 0.340 Angle : 1.051 11.340 4297 Z= 0.584 Chirality : 0.059 0.197 451 Planarity : 0.008 0.064 506 Dihedral : 16.243 87.883 1251 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.33 % Allowed : 14.29 % Favored : 85.38 % 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: -2.71 (0.41), residues: 337 helix: -2.26 (0.37), residues: 116 sheet: -1.88 (0.68), residues: 51 loop : -1.29 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 266 HIS 0.002 0.001 HIS A 71 PHE 0.010 0.002 PHE A 293 TYR 0.015 0.002 TYR A 321 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.4145 (m100) cc_final: 0.3613 (m100) REVERT: A 87 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5065 (mtt180) REVERT: A 91 PHE cc_start: 0.6079 (t80) cc_final: 0.5870 (t80) REVERT: A 95 LYS cc_start: 0.7872 (tttt) cc_final: 0.6654 (mmmt) REVERT: A 137 ILE cc_start: 0.6298 (mm) cc_final: 0.5943 (tp) REVERT: A 147 LYS cc_start: 0.5333 (mmtt) cc_final: 0.5107 (tptt) REVERT: A 158 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6955 (mm-30) REVERT: A 176 SER cc_start: 0.4986 (m) cc_final: 0.4551 (p) REVERT: A 177 GLU cc_start: 0.6151 (tt0) cc_final: 0.5704 (mp0) REVERT: A 183 PRO cc_start: 0.5777 (Cg_exo) cc_final: 0.5370 (Cg_endo) REVERT: A 197 ARG cc_start: 0.5058 (tpt170) cc_final: 0.4838 (tpt170) REVERT: A 238 ASP cc_start: 0.6641 (m-30) cc_final: 0.6287 (t0) REVERT: A 258 VAL cc_start: 0.7790 (t) cc_final: 0.7587 (t) REVERT: A 264 ARG cc_start: 0.6642 (ptt180) cc_final: 0.6262 (ptt180) REVERT: A 266 TRP cc_start: 0.7664 (m100) cc_final: 0.7348 (m100) REVERT: A 267 VAL cc_start: 0.7865 (t) cc_final: 0.7545 (t) REVERT: A 279 LYS cc_start: 0.8305 (tttt) cc_final: 0.7956 (mtpp) REVERT: A 292 MET cc_start: 0.8457 (tmm) cc_final: 0.8071 (tpt) REVERT: A 322 MET cc_start: 0.7559 (mmt) cc_final: 0.7007 (ptp) REVERT: A 334 MET cc_start: 0.1537 (mmt) cc_final: 0.0137 (ttp) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2075 time to fit residues: 23.1919 Evaluate side-chains 51 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3142 Z= 0.252 Angle : 0.722 8.865 4297 Z= 0.371 Chirality : 0.048 0.179 451 Planarity : 0.007 0.056 506 Dihedral : 15.154 79.437 519 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.99 % Allowed : 16.61 % Favored : 81.40 % 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: -1.37 (0.43), residues: 337 helix: -0.33 (0.47), residues: 109 sheet: -1.93 (0.70), residues: 52 loop : -0.86 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 294 HIS 0.005 0.001 HIS A 64 PHE 0.015 0.003 PHE A 241 TYR 0.011 0.002 TYR A 54 ARG 0.003 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6559 (tmt-80) cc_final: 0.4298 (mtt180) REVERT: A 95 LYS cc_start: 0.7995 (tttt) cc_final: 0.7070 (tppt) REVERT: A 147 LYS cc_start: 0.5676 (mmtt) cc_final: 0.5448 (tptt) REVERT: A 153 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7226 (tp) REVERT: A 158 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7064 (mm-30) REVERT: A 176 SER cc_start: 0.5708 (m) cc_final: 0.5357 (p) REVERT: A 177 GLU cc_start: 0.5898 (tt0) cc_final: 0.5456 (mp0) REVERT: A 238 ASP cc_start: 0.7089 (m-30) cc_final: 0.6621 (t0) REVERT: A 242 ILE cc_start: 0.8332 (mm) cc_final: 0.8130 (tp) REVERT: A 266 TRP cc_start: 0.7219 (m100) cc_final: 0.6003 (m100) REVERT: A 273 ARG cc_start: 0.3614 (mtt180) cc_final: 0.1738 (ttt180) REVERT: A 279 LYS cc_start: 0.8241 (tttt) cc_final: 0.7846 (mtpp) REVERT: A 305 ASN cc_start: 0.7638 (t0) cc_final: 0.7429 (m-40) REVERT: A 319 MET cc_start: 0.7722 (mpp) cc_final: 0.7457 (mpp) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.2409 time to fit residues: 15.1463 Evaluate side-chains 45 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3142 Z= 0.289 Angle : 0.758 6.460 4297 Z= 0.398 Chirality : 0.049 0.183 451 Planarity : 0.008 0.096 506 Dihedral : 15.652 82.805 515 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.98 % Allowed : 17.28 % Favored : 77.74 % 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: -1.50 (0.43), residues: 337 helix: -0.23 (0.46), residues: 118 sheet: -1.90 (0.60), residues: 62 loop : -1.07 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 266 HIS 0.006 0.003 HIS A 64 PHE 0.009 0.002 PHE A 11 TYR 0.015 0.002 TYR A 13 ARG 0.004 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.4342 (mtt180) REVERT: A 95 LYS cc_start: 0.8139 (tttt) cc_final: 0.7245 (tppt) REVERT: A 147 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5731 (mmtt) REVERT: A 149 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6693 (mtmt) REVERT: A 153 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7091 (tp) REVERT: A 175 ILE cc_start: 0.0145 (OUTLIER) cc_final: -0.0466 (tp) REVERT: A 177 GLU cc_start: 0.5939 (tt0) cc_final: 0.5354 (mp0) REVERT: A 238 ASP cc_start: 0.7344 (m-30) cc_final: 0.6615 (t0) REVERT: A 266 TRP cc_start: 0.7115 (m100) cc_final: 0.5844 (m100) REVERT: A 279 LYS cc_start: 0.8259 (tttt) cc_final: 0.7714 (mtpp) REVERT: A 305 ASN cc_start: 0.7422 (t0) cc_final: 0.7173 (m-40) REVERT: A 310 LYS cc_start: 0.8155 (mttt) cc_final: 0.7822 (mmmt) REVERT: A 319 MET cc_start: 0.7947 (mpp) cc_final: 0.7577 (mpp) outliers start: 15 outliers final: 7 residues processed: 54 average time/residue: 0.2814 time to fit residues: 17.3163 Evaluate side-chains 47 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.0070 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3142 Z= 0.150 Angle : 0.595 6.816 4297 Z= 0.304 Chirality : 0.045 0.153 451 Planarity : 0.006 0.058 506 Dihedral : 14.907 82.886 515 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.32 % Allowed : 17.94 % Favored : 78.74 % 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: -1.05 (0.43), residues: 337 helix: 0.41 (0.47), residues: 110 sheet: -1.68 (0.64), residues: 63 loop : -0.97 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 294 HIS 0.005 0.001 HIS A 134 PHE 0.010 0.002 PHE A 260 TYR 0.008 0.001 TYR A 185 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6636 (tmt-80) cc_final: 0.4347 (mtt180) REVERT: A 95 LYS cc_start: 0.8028 (tttt) cc_final: 0.7025 (tppt) REVERT: A 149 LYS cc_start: 0.6826 (mtmm) cc_final: 0.6447 (mtmm) REVERT: A 153 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7199 (tp) REVERT: A 177 GLU cc_start: 0.5797 (tt0) cc_final: 0.5301 (mp0) REVERT: A 238 ASP cc_start: 0.6851 (m-30) cc_final: 0.6402 (t0) REVERT: A 243 GLU cc_start: 0.8200 (pm20) cc_final: 0.7996 (pm20) REVERT: A 266 TRP cc_start: 0.7237 (m100) cc_final: 0.5932 (m100) REVERT: A 279 LYS cc_start: 0.8290 (tttt) cc_final: 0.7803 (mtpp) REVERT: A 292 MET cc_start: 0.8381 (tmm) cc_final: 0.7719 (tmm) REVERT: A 319 MET cc_start: 0.7945 (mpp) cc_final: 0.7528 (mpp) REVERT: A 334 MET cc_start: 0.1019 (OUTLIER) cc_final: -0.0370 (ttp) outliers start: 10 outliers final: 2 residues processed: 50 average time/residue: 0.2442 time to fit residues: 14.1828 Evaluate side-chains 39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 0.0010 chunk 6 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3142 Z= 0.143 Angle : 0.586 6.754 4297 Z= 0.299 Chirality : 0.043 0.132 451 Planarity : 0.006 0.053 506 Dihedral : 14.659 84.145 515 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.00 % Allowed : 20.60 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.44), residues: 337 helix: 0.75 (0.48), residues: 111 sheet: -1.63 (0.65), residues: 58 loop : -0.93 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 53 HIS 0.005 0.001 HIS A 134 PHE 0.009 0.001 PHE A 194 TYR 0.009 0.001 TYR A 213 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.405 Fit side-chains REVERT: A 95 LYS cc_start: 0.8008 (tttt) cc_final: 0.7090 (tppt) REVERT: A 149 LYS cc_start: 0.6889 (mtmm) cc_final: 0.6444 (mtmm) REVERT: A 153 LEU cc_start: 0.7422 (mp) cc_final: 0.7124 (tp) REVERT: A 177 GLU cc_start: 0.5801 (tt0) cc_final: 0.5282 (mp0) REVERT: A 238 ASP cc_start: 0.6699 (m-30) cc_final: 0.6231 (t0) REVERT: A 279 LYS cc_start: 0.8272 (tttt) cc_final: 0.7775 (mtpp) REVERT: A 292 MET cc_start: 0.8371 (tmm) cc_final: 0.7781 (tmm) REVERT: A 305 ASN cc_start: 0.7525 (t0) cc_final: 0.7291 (m-40) REVERT: A 319 MET cc_start: 0.7889 (mpp) cc_final: 0.7539 (mpp) REVERT: A 322 MET cc_start: 0.6752 (ptt) cc_final: 0.6506 (ptp) REVERT: A 334 MET cc_start: 0.1848 (mmt) cc_final: 0.0398 (ttp) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.1901 time to fit residues: 10.9580 Evaluate side-chains 42 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 0.0980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3142 Z= 0.170 Angle : 0.609 6.594 4297 Z= 0.312 Chirality : 0.044 0.146 451 Planarity : 0.006 0.052 506 Dihedral : 14.797 84.557 515 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.33 % Allowed : 21.59 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.44), residues: 337 helix: 0.88 (0.50), residues: 111 sheet: -1.60 (0.60), residues: 63 loop : -0.99 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 150 HIS 0.007 0.001 HIS A 134 PHE 0.007 0.001 PHE A 260 TYR 0.009 0.001 TYR A 54 ARG 0.005 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.419 Fit side-chains REVERT: A 95 LYS cc_start: 0.7937 (tttt) cc_final: 0.6947 (tppt) REVERT: A 149 LYS cc_start: 0.6875 (mtmm) cc_final: 0.6462 (mtmm) REVERT: A 153 LEU cc_start: 0.7505 (mp) cc_final: 0.7217 (tp) REVERT: A 177 GLU cc_start: 0.5544 (tt0) cc_final: 0.5116 (mp0) REVERT: A 238 ASP cc_start: 0.6926 (m-30) cc_final: 0.6442 (t0) REVERT: A 243 GLU cc_start: 0.8371 (pm20) cc_final: 0.8123 (pm20) REVERT: A 279 LYS cc_start: 0.8266 (tttt) cc_final: 0.7748 (mtpp) REVERT: A 292 MET cc_start: 0.8350 (tmm) cc_final: 0.7719 (tmm) REVERT: A 319 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7369 (mpp) REVERT: A 322 MET cc_start: 0.6679 (ptt) cc_final: 0.6449 (ptp) REVERT: A 334 MET cc_start: 0.1480 (OUTLIER) cc_final: 0.0027 (ttp) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.1918 time to fit residues: 9.7708 Evaluate side-chains 41 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3142 Z= 0.157 Angle : 0.596 6.783 4297 Z= 0.303 Chirality : 0.044 0.137 451 Planarity : 0.006 0.052 506 Dihedral : 14.772 86.213 515 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.33 % Allowed : 24.25 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.44), residues: 337 helix: 0.93 (0.49), residues: 111 sheet: -1.54 (0.62), residues: 58 loop : -1.02 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 150 HIS 0.005 0.001 HIS A 134 PHE 0.007 0.001 PHE A 194 TYR 0.009 0.001 TYR A 185 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7914 (tttt) cc_final: 0.6784 (mmmt) REVERT: A 149 LYS cc_start: 0.6825 (mtmm) cc_final: 0.6416 (mtmm) REVERT: A 153 LEU cc_start: 0.7391 (mp) cc_final: 0.7046 (tp) REVERT: A 177 GLU cc_start: 0.5581 (tt0) cc_final: 0.5148 (mp0) REVERT: A 238 ASP cc_start: 0.6934 (m-30) cc_final: 0.6420 (t0) REVERT: A 279 LYS cc_start: 0.8199 (tttt) cc_final: 0.7752 (mtpp) REVERT: A 292 MET cc_start: 0.8298 (tmm) cc_final: 0.7664 (tmm) REVERT: A 319 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7391 (mpp) REVERT: A 334 MET cc_start: 0.1345 (OUTLIER) cc_final: -0.0110 (ttp) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.2147 time to fit residues: 12.0287 Evaluate side-chains 41 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3142 Z= 0.161 Angle : 0.600 6.772 4297 Z= 0.308 Chirality : 0.045 0.141 451 Planarity : 0.006 0.051 506 Dihedral : 14.705 86.692 515 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.66 % Allowed : 24.25 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.44), residues: 337 helix: 0.94 (0.50), residues: 111 sheet: -1.47 (0.62), residues: 58 loop : -1.04 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 150 HIS 0.004 0.001 HIS A 134 PHE 0.007 0.001 PHE A 81 TYR 0.009 0.001 TYR A 54 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7910 (tttt) cc_final: 0.6765 (mmmt) REVERT: A 149 LYS cc_start: 0.6687 (mtmm) cc_final: 0.6439 (mtmm) REVERT: A 177 GLU cc_start: 0.5589 (tt0) cc_final: 0.5163 (mp0) REVERT: A 238 ASP cc_start: 0.6980 (m-30) cc_final: 0.6444 (t0) REVERT: A 279 LYS cc_start: 0.8196 (tttt) cc_final: 0.7746 (mtpp) REVERT: A 292 MET cc_start: 0.8299 (tmm) cc_final: 0.7986 (tmm) REVERT: A 319 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7356 (mpp) REVERT: A 334 MET cc_start: 0.1361 (OUTLIER) cc_final: -0.0109 (ttp) outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 0.2411 time to fit residues: 11.4815 Evaluate side-chains 40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 2 optimal weight: 9.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3142 Z= 0.155 Angle : 0.601 7.297 4297 Z= 0.307 Chirality : 0.044 0.131 451 Planarity : 0.005 0.051 506 Dihedral : 14.368 86.949 515 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.00 % Allowed : 25.58 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.44), residues: 337 helix: 1.09 (0.50), residues: 109 sheet: -1.28 (0.64), residues: 58 loop : -1.17 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 150 HIS 0.005 0.001 HIS A 134 PHE 0.010 0.001 PHE A 194 TYR 0.012 0.001 TYR A 321 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.393 Fit side-chains REVERT: A 18 HIS cc_start: 0.8059 (m-70) cc_final: 0.6929 (p-80) REVERT: A 95 LYS cc_start: 0.8052 (tttt) cc_final: 0.6949 (mmmt) REVERT: A 177 GLU cc_start: 0.5573 (tt0) cc_final: 0.5186 (mp0) REVERT: A 238 ASP cc_start: 0.6897 (m-30) cc_final: 0.6339 (t0) REVERT: A 279 LYS cc_start: 0.8180 (tttt) cc_final: 0.7732 (mtpp) REVERT: A 292 MET cc_start: 0.8546 (tmm) cc_final: 0.8310 (tmm) REVERT: A 319 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7222 (mpp) REVERT: A 322 MET cc_start: 0.6993 (mtm) cc_final: 0.6594 (mtm) REVERT: A 334 MET cc_start: 0.2277 (mmt) cc_final: 0.0597 (ttp) outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 0.1881 time to fit residues: 10.4029 Evaluate side-chains 43 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 0.3980 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3142 Z= 0.168 Angle : 0.631 7.575 4297 Z= 0.326 Chirality : 0.046 0.159 451 Planarity : 0.006 0.051 506 Dihedral : 14.188 86.147 515 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.00 % Allowed : 25.91 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.44), residues: 337 helix: 1.07 (0.51), residues: 108 sheet: -1.26 (0.64), residues: 58 loop : -1.31 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 150 HIS 0.005 0.001 HIS A 134 PHE 0.014 0.001 PHE A 31 TYR 0.021 0.001 TYR A 54 ARG 0.003 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.359 Fit side-chains REVERT: A 18 HIS cc_start: 0.8010 (m-70) cc_final: 0.6866 (p-80) REVERT: A 95 LYS cc_start: 0.7901 (tttt) cc_final: 0.6752 (mmmt) REVERT: A 177 GLU cc_start: 0.5594 (tt0) cc_final: 0.5234 (mp0) REVERT: A 238 ASP cc_start: 0.6796 (m-30) cc_final: 0.6173 (t0) REVERT: A 255 LEU cc_start: 0.6428 (pt) cc_final: 0.6100 (mp) REVERT: A 279 LYS cc_start: 0.8220 (tttt) cc_final: 0.7767 (mtpp) REVERT: A 292 MET cc_start: 0.8551 (tmm) cc_final: 0.8256 (tmm) REVERT: A 319 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7281 (mpp) REVERT: A 322 MET cc_start: 0.6993 (mtm) cc_final: 0.6594 (mtm) REVERT: A 334 MET cc_start: 0.1749 (mmt) cc_final: 0.0142 (ttp) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1634 time to fit residues: 8.0062 Evaluate side-chains 37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 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 = 0.4374 r_free = 0.4374 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.114345 restraints weight = 12088.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.114115 restraints weight = 9864.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.114433 restraints weight = 8032.013| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3142 Z= 0.168 Angle : 0.649 7.445 4297 Z= 0.335 Chirality : 0.046 0.151 451 Planarity : 0.006 0.051 506 Dihedral : 14.018 87.054 515 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.00 % Allowed : 26.25 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.44), residues: 337 helix: 0.91 (0.51), residues: 109 sheet: -1.27 (0.63), residues: 58 loop : -1.41 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 150 HIS 0.003 0.001 HIS A 134 PHE 0.012 0.001 PHE A 31 TYR 0.019 0.001 TYR A 54 ARG 0.003 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1164.18 seconds wall clock time: 22 minutes 49.74 seconds (1369.74 seconds total)