Starting phenix.real_space_refine on Thu Mar 6 03:26:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vac_43088/03_2025/8vac_43088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vac_43088/03_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_43088/03_2025/8vac_43088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vac_43088/03_2025/8vac_43088.map" model { file = "/net/cci-nas-00/data/ceres_data/8vac_43088/03_2025/8vac_43088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vac_43088/03_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-5624/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: 4.52, per 1000 atoms: 0.97 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: 1.75 Conformation dependent library (CDL) restraints added in 555.7 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: 0.45 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: 1.28 Time building geometry restraints manager: 1.36 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: 6.460 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 16.540 Find NCS groups from input model: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- 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 : 0.556 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: 0.1434 time to fit residues: 10.8592 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 : 0.551 ------------------------------------------------------------------------------- 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 = 0.099445 restraints weight = 7792.287| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.71 r_work: 0.3164 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.545 Fit side-chains REVERT: A 520 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8320 (mm-30) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1192 time to fit residues: 8.4433 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 : 0.545 ------------------------------------------------------------------------------- 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: 0.8980 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.121985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095806 restraints weight = 7967.421| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.84 r_work: 0.3095 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4766 Z= 0.248 Angle : 0.589 7.605 6437 Z= 0.301 Chirality : 0.041 0.178 716 Planarity : 0.004 0.033 832 Dihedral : 5.627 43.531 699 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.97 % Allowed : 13.98 % Favored : 84.06 % 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: 1.69 (0.36), residues: 579 helix: 1.64 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -0.02 (0.52), residues: 171 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 0.012 0.002 PHE A 554 TYR 0.018 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 : 0.492 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.1065 time to fit residues: 9.1179 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: 0.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.122198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095988 restraints weight = 7921.745| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.85 r_work: 0.3093 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4766 Z= 0.229 Angle : 0.565 6.729 6437 Z= 0.292 Chirality : 0.040 0.175 716 Planarity : 0.004 0.032 832 Dihedral : 4.980 29.603 699 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.36 % Allowed : 15.35 % Favored : 82.28 % 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 (0.37), residues: 579 helix: 1.63 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.03 (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 0.017 0.002 TYR A 161 ARG 0.004 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 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.577 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 0.1084 time to fit residues: 8.9548 Evaluate side-chains 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.120044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094125 restraints weight = 7974.383| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.79 r_work: 0.3066 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4766 Z= 0.262 Angle : 0.586 8.175 6437 Z= 0.300 Chirality : 0.041 0.170 716 Planarity : 0.004 0.031 832 Dihedral : 4.705 22.233 699 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.76 % Allowed : 17.91 % Favored : 79.33 % 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: 1.58 (0.37), residues: 579 helix: 1.55 (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 0.012 0.002 PHE A 554 TYR 0.019 0.002 TYR A 161 ARG 0.005 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 54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7810 (pm20) outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.1058 time to fit residues: 8.5211 Evaluate side-chains 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 0.0030 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 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: 2.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.123183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097641 restraints weight = 7962.706| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.81 r_work: 0.3123 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4766 Z= 0.194 Angle : 0.544 7.966 6437 Z= 0.279 Chirality : 0.039 0.152 716 Planarity : 0.003 0.032 832 Dihedral : 4.473 22.231 699 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.95 % Allowed : 18.90 % Favored : 78.15 % 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: 1.65 (0.37), residues: 579 helix: 1.60 (0.26), residues: 415 sheet: None (None), residues: 0 loop : -0.08 (0.54), residues: 164 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 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 63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7685 (pm20) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.1286 time to fit residues: 11.3810 Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 32 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.122891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097140 restraints weight = 7965.183| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.82 r_work: 0.3111 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4766 Z= 0.199 Angle : 0.578 9.179 6437 Z= 0.292 Chirality : 0.040 0.179 716 Planarity : 0.003 0.033 832 Dihedral : 4.432 26.666 699 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.56 % Allowed : 19.29 % Favored : 78.15 % 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: 1.71 (0.37), residues: 579 helix: 1.58 (0.26), residues: 420 sheet: None (None), residues: 0 loop : 0.10 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.014 0.001 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 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 245 CYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8399 (t) REVERT: A 397 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: A 551 PHE cc_start: 0.8358 (m-80) cc_final: 0.7701 (t80) outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.1265 time to fit residues: 10.0626 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 245 CYS Chi-restraints excluded: chain A residue 265 CYS 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 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: 0.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.122755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096945 restraints weight = 7971.952| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.82 r_work: 0.3111 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4766 Z= 0.212 Angle : 0.578 7.713 6437 Z= 0.292 Chirality : 0.040 0.179 716 Planarity : 0.004 0.033 832 Dihedral : 4.381 27.303 699 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.15 % Allowed : 19.49 % Favored : 77.36 % 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: 1.71 (0.37), residues: 579 helix: 1.56 (0.26), residues: 421 sheet: None (None), residues: 0 loop : 0.12 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.014 0.002 TYR A 161 ARG 0.004 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 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 245 CYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8419 (t) REVERT: A 397 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: A 551 PHE cc_start: 0.8327 (m-80) cc_final: 0.7705 (t80) outliers start: 16 outliers final: 13 residues processed: 58 average time/residue: 0.1205 time to fit residues: 10.1899 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 245 CYS 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 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: 0.8980 chunk 11 optimal weight: 0.0060 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 0.0040 chunk 47 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.124389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099139 restraints weight = 7898.504| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.75 r_work: 0.3157 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4766 Z= 0.175 Angle : 0.570 7.714 6437 Z= 0.286 Chirality : 0.039 0.168 716 Planarity : 0.003 0.034 832 Dihedral : 4.345 26.369 699 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.15 % Allowed : 19.69 % Favored : 77.17 % 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: 1.74 (0.37), residues: 579 helix: 1.66 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.06 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 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 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 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 245 CYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8362 (t) REVERT: A 397 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: A 551 PHE cc_start: 0.8294 (m-80) cc_final: 0.7733 (t80) outliers start: 16 outliers final: 13 residues processed: 58 average time/residue: 0.1168 time to fit residues: 10.0967 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 245 CYS 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 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: 0.0970 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.123837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098516 restraints weight = 7911.581| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.75 r_work: 0.3149 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4766 Z= 0.194 Angle : 0.584 7.893 6437 Z= 0.293 Chirality : 0.040 0.249 716 Planarity : 0.004 0.034 832 Dihedral : 4.357 26.275 699 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.95 % Allowed : 20.08 % Favored : 76.97 % 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: 1.71 (0.36), residues: 579 helix: 1.64 (0.26), residues: 415 sheet: None (None), residues: 0 loop : -0.05 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A 554 TYR 0.014 0.002 TYR A 161 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 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 245 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8394 (t) REVERT: A 397 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7707 (pm20) outliers start: 15 outliers final: 13 residues processed: 55 average time/residue: 0.1174 time to fit residues: 9.4689 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 : 0.523 ------------------------------------------------------------------------------- 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 245 CYS 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 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: 0.5980 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.123859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098498 restraints weight = 7947.855| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.76 r_work: 0.3147 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4766 Z= 0.203 Angle : 0.587 7.657 6437 Z= 0.297 Chirality : 0.040 0.240 716 Planarity : 0.004 0.034 832 Dihedral : 4.361 26.046 699 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.15 % Allowed : 20.08 % Favored : 76.77 % 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: 1.62 (0.36), residues: 579 helix: 1.54 (0.26), residues: 420 sheet: None (None), residues: 0 loop : -0.03 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2397.95 seconds wall clock time: 42 minutes 7.84 seconds (2527.84 seconds total)