Starting phenix.real_space_refine on Tue Jan 14 00:19:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vac_43088/01_2025/8vac_43088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vac_43088/01_2025/8vac_43088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vac_43088/01_2025/8vac_43088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vac_43088/01_2025/8vac_43088.map" model { file = "/net/cci-nas-00/data/ceres_data/8vac_43088/01_2025/8vac_43088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vac_43088/01_2025/8vac_43088.cif" } resolution = 3.4 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 2950 2.51 5 N 782 2.21 5 O 895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4669 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4623 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 556} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'9TP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.49, per 1000 atoms: 0.96 Number of scatterers: 4669 At special positions: 0 Unit cell: (67.354, 89.994, 95.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 895 8.00 N 782 7.00 C 2950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 101 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 279 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 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: 1.25 Conformation dependent library (CDL) restraints added in 592.3 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 15 through 31 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 65 through 76 removed outlier: 4.073A pdb=" N THR A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 removed outlier: 4.339A pdb=" N LEU A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 80' Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.997A pdb=" N CYS A 90 " --> pdb=" O MET A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.684A pdb=" N GLU A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.577A pdb=" N PHE A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 174 through 207 removed outlier: 3.513A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.771A pdb=" N GLY A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 223 removed outlier: 3.825A pdb=" N PHE A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 247 Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.997A pdb=" N LYS A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 322 through 338 removed outlier: 3.526A pdb=" N PHE A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.285A pdb=" N TYR A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 371 " --> pdb=" O HIS A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 415 removed outlier: 4.112A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.872A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N TYR A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 438 removed outlier: 4.014A pdb=" N GLY A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.989A pdb=" N CYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 517 through 536 Processing helix chain 'A' and resid 540 through 558 Processing helix chain 'A' and resid 563 through 582 319 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 815 1.30 - 1.43: 1163 1.43 - 1.56: 2734 1.56 - 1.70: 5 1.70 - 1.83: 49 Bond restraints: 4766 Sorted by residual: bond pdb=" C14 9TP A 601 " pdb=" O15 9TP A 601 " ideal model delta sigma weight residual 1.337 1.640 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C14 9TP A 601 " pdb=" C8 9TP A 601 " ideal model delta sigma weight residual 1.505 1.217 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C8 9TP A 601 " pdb=" C9 9TP A 601 " ideal model delta sigma weight residual 1.513 1.800 -0.287 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C16 9TP A 601 " pdb=" C9 9TP A 601 " ideal model delta sigma weight residual 1.519 1.297 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C4 9TP A 601 " pdb=" C5 9TP A 601 " ideal model delta sigma weight residual 1.393 1.609 -0.216 2.00e-02 2.50e+03 1.17e+02 ... (remaining 4761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 6360 3.10 - 6.21: 65 6.21 - 9.31: 10 9.31 - 12.42: 1 12.42 - 15.52: 1 Bond angle restraints: 6437 Sorted by residual: angle pdb=" C40 9TP A 601 " pdb=" S1 9TP A 601 " pdb=" C42 9TP A 601 " ideal model delta sigma weight residual 91.72 107.24 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C ALA A 364 " pdb=" CA ALA A 364 " pdb=" CB ALA A 364 " ideal model delta sigma weight residual 115.79 110.65 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C LYS A 359 " pdb=" N CYS A 360 " pdb=" CA CYS A 360 " ideal model delta sigma weight residual 122.42 116.20 6.22 1.77e+00 3.19e-01 1.23e+01 angle pdb=" C MET A 123 " pdb=" N CYS A 124 " pdb=" CA CYS A 124 " ideal model delta sigma weight residual 122.06 115.54 6.52 1.86e+00 2.89e-01 1.23e+01 angle pdb=" C ALA A 553 " pdb=" N PHE A 554 " pdb=" CA PHE A 554 " ideal model delta sigma weight residual 120.68 114.75 5.93 1.70e+00 3.46e-01 1.22e+01 ... (remaining 6432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 2648 17.43 - 34.86: 323 34.86 - 52.28: 61 52.28 - 69.71: 12 69.71 - 87.14: 12 Dihedral angle restraints: 3056 sinusoidal: 1318 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS A 360 " pdb=" SG CYS A 360 " pdb=" SG CYS A 369 " pdb=" CB CYS A 369 " ideal model delta sinusoidal sigma weight residual 93.00 175.67 -82.67 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CA CYS A 168 " pdb=" C CYS A 168 " pdb=" N CYS A 169 " pdb=" CA CYS A 169 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual -86.00 -41.68 -44.32 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 3053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 579 0.051 - 0.102: 110 0.102 - 0.153: 19 0.153 - 0.204: 3 0.204 - 0.254: 5 Chirality restraints: 716 Sorted by residual: chirality pdb=" C7 9TP A 601 " pdb=" C17 9TP A 601 " pdb=" C4 9TP A 601 " pdb=" C8 9TP A 601 " both_signs ideal model delta sigma weight residual False 2.52 2.78 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C8 9TP A 601 " pdb=" C14 9TP A 601 " pdb=" C7 9TP A 601 " pdb=" C9 9TP A 601 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C38 9TP A 601 " pdb=" C40 9TP A 601 " pdb=" O37 9TP A 601 " pdb=" O39 9TP A 601 " both_signs ideal model delta sigma weight residual False 2.26 2.51 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 713 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 485 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 486 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 117 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ARG A 117 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG A 117 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO A 118 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 95 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 96 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.017 5.00e-02 4.00e+02 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 874 2.77 - 3.30: 4771 3.30 - 3.83: 7977 3.83 - 4.37: 8909 4.37 - 4.90: 15393 Nonbonded interactions: 37924 Sorted by model distance: nonbonded pdb=" OG SER A 312 " pdb=" OD1 ASP A 314 " model vdw 2.232 3.040 nonbonded pdb=" O PRO A 113 " pdb=" NH2 ARG A 145 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASP A 121 " pdb=" NZ LYS A 174 " model vdw 2.322 3.120 nonbonded pdb=" OD1 ASP A 471 " pdb=" N ARG A 472 " model vdw 2.338 3.120 nonbonded pdb=" NH2 ARG A 348 " pdb=" OE2 GLU A 450 " model vdw 2.355 3.120 ... (remaining 37919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.670 Find NCS groups from input model: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.303 4766 Z= 0.810 Angle : 0.786 15.524 6437 Z= 0.375 Chirality : 0.046 0.254 716 Planarity : 0.004 0.041 832 Dihedral : 15.868 87.141 1865 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.17 (0.36), residues: 579 helix: 1.21 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.16 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.023 0.002 PHE A 502 TYR 0.014 0.002 TYR A 150 ARG 0.008 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.578 Fit side-chains REVERT: A 408 LEU cc_start: 0.9162 (tp) cc_final: 0.8938 (tt) REVERT: A 520 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7772 (mt-10) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1522 time to fit residues: 11.5349 Evaluate side-chains 42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 405 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099446 restraints weight = 7792.287| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.71 r_work: 0.3165 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4766 Z= 0.232 Angle : 0.617 7.622 6437 Z= 0.311 Chirality : 0.041 0.171 716 Planarity : 0.004 0.036 832 Dihedral : 6.319 52.334 699 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.98 % Allowed : 8.86 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.45 (0.36), residues: 579 helix: 1.44 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.13 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 146 PHE 0.014 0.002 PHE A 554 TYR 0.017 0.002 TYR A 452 ARG 0.005 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.609 Fit side-chains REVERT: A 520 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8319 (mm-30) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1264 time to fit residues: 8.9440 Evaluate side-chains 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 474 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 405 ASN A 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095520 restraints weight = 7970.055| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.84 r_work: 0.3090 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4766 Z= 0.251 Angle : 0.592 7.701 6437 Z= 0.303 Chirality : 0.042 0.181 716 Planarity : 0.004 0.033 832 Dihedral : 5.610 43.294 699 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.97 % Allowed : 14.17 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.68 (0.36), residues: 579 helix: 1.63 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -0.03 (0.52), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.006 0.001 HIS A 146 PHE 0.013 0.002 PHE A 554 TYR 0.019 0.002 TYR A 150 ARG 0.005 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.529 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.1131 time to fit residues: 9.7309 Evaluate side-chains 44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 36 optimal weight: 0.0050 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098226 restraints weight = 7874.297| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.86 r_work: 0.3128 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4766 Z= 0.177 Angle : 0.536 6.429 6437 Z= 0.277 Chirality : 0.039 0.162 716 Planarity : 0.003 0.032 832 Dihedral : 4.856 27.430 699 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.36 % Allowed : 15.75 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.81 (0.37), residues: 579 helix: 1.73 (0.26), residues: 409 sheet: None (None), residues: 0 loop : 0.00 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.014 0.001 PHE A 554 TYR 0.014 0.001 TYR A 161 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.591 Fit side-chains REVERT: A 245 CYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8439 (t) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 0.1200 time to fit residues: 10.3288 Evaluate side-chains 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095891 restraints weight = 8022.463| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.88 r_work: 0.3087 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4766 Z= 0.217 Angle : 0.571 7.954 6437 Z= 0.288 Chirality : 0.040 0.153 716 Planarity : 0.004 0.031 832 Dihedral : 4.593 22.355 699 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.95 % Allowed : 18.11 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.37), residues: 579 helix: 1.70 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.05 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.016 0.002 TYR A 161 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7728 (pm20) outliers start: 15 outliers final: 11 residues processed: 58 average time/residue: 0.1135 time to fit residues: 9.9701 Evaluate side-chains 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 476 CYS Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095659 restraints weight = 7987.163| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.83 r_work: 0.3095 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4766 Z= 0.250 Angle : 0.584 8.052 6437 Z= 0.297 Chirality : 0.040 0.159 716 Planarity : 0.004 0.035 832 Dihedral : 4.539 23.474 699 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.76 % Allowed : 19.49 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.37), residues: 579 helix: 1.56 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.09 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.002 PHE A 554 TYR 0.016 0.002 TYR A 161 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7761 (pm20) outliers start: 14 outliers final: 12 residues processed: 57 average time/residue: 0.1135 time to fit residues: 9.6622 Evaluate side-chains 52 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096797 restraints weight = 7988.144| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.84 r_work: 0.3113 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4766 Z= 0.188 Angle : 0.552 7.775 6437 Z= 0.280 Chirality : 0.039 0.153 716 Planarity : 0.003 0.031 832 Dihedral : 4.362 23.664 699 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.95 % Allowed : 19.09 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.37), residues: 579 helix: 1.66 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.08 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.014 0.002 TYR A 161 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: A 551 PHE cc_start: 0.8352 (m-80) cc_final: 0.7730 (t80) outliers start: 15 outliers final: 12 residues processed: 55 average time/residue: 0.1218 time to fit residues: 9.5931 Evaluate side-chains 53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.0470 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 440 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099284 restraints weight = 7961.664| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.77 r_work: 0.3156 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4766 Z= 0.159 Angle : 0.538 7.677 6437 Z= 0.274 Chirality : 0.038 0.168 716 Planarity : 0.003 0.030 832 Dihedral : 4.255 24.265 699 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.95 % Allowed : 19.09 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.87 (0.37), residues: 579 helix: 1.74 (0.26), residues: 415 sheet: None (None), residues: 0 loop : 0.06 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A 554 TYR 0.013 0.001 TYR A 140 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: A 551 PHE cc_start: 0.8287 (m-80) cc_final: 0.7733 (t80) outliers start: 15 outliers final: 13 residues processed: 55 average time/residue: 0.1206 time to fit residues: 9.6758 Evaluate side-chains 54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 47 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099556 restraints weight = 7885.536| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.75 r_work: 0.3168 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4766 Z= 0.158 Angle : 0.551 7.756 6437 Z= 0.277 Chirality : 0.039 0.172 716 Planarity : 0.003 0.029 832 Dihedral : 4.195 24.230 699 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.95 % Allowed : 19.09 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.91 (0.36), residues: 579 helix: 1.69 (0.26), residues: 419 sheet: None (None), residues: 0 loop : 0.30 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A 554 TYR 0.013 0.002 TYR A 452 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7582 (pm20) outliers start: 15 outliers final: 13 residues processed: 54 average time/residue: 0.1208 time to fit residues: 9.6214 Evaluate side-chains 53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099296 restraints weight = 7867.905| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.78 r_work: 0.3161 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4766 Z= 0.164 Angle : 0.561 8.483 6437 Z= 0.283 Chirality : 0.039 0.257 716 Planarity : 0.003 0.029 832 Dihedral : 4.247 25.325 699 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.95 % Allowed : 19.29 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.36), residues: 579 helix: 1.74 (0.26), residues: 414 sheet: None (None), residues: 0 loop : 0.13 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A 554 TYR 0.014 0.001 TYR A 140 ARG 0.003 0.000 ARG A 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: A 551 PHE cc_start: 0.8374 (m-80) cc_final: 0.7734 (t80) outliers start: 15 outliers final: 14 residues processed: 55 average time/residue: 0.1167 time to fit residues: 9.4038 Evaluate side-chains 55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.0060 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100632 restraints weight = 7918.457| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.76 r_work: 0.3183 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4766 Z= 0.155 Angle : 0.557 8.004 6437 Z= 0.280 Chirality : 0.039 0.253 716 Planarity : 0.003 0.029 832 Dihedral : 4.218 24.893 699 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.76 % Allowed : 19.69 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.37), residues: 579 helix: 1.70 (0.26), residues: 418 sheet: None (None), residues: 0 loop : 0.19 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A 554 TYR 0.013 0.001 TYR A 140 ARG 0.003 0.000 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.80 seconds wall clock time: 42 minutes 59.40 seconds (2579.40 seconds total)