Starting phenix.real_space_refine on Sat May 10 02:22:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vac_43088/05_2025/8vac_43088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vac_43088/05_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_43088/05_2025/8vac_43088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vac_43088/05_2025/8vac_43088.map" model { file = "/net/cci-nas-00/data/ceres_data/8vac_43088/05_2025/8vac_43088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vac_43088/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.02, per 1000 atoms: 1.08 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: 1.33 Conformation dependent library (CDL) restraints added in 575.4 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: 0.54 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: 1.31 Time building geometry restraints manager: 1.51 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- 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 4783 Z= 0.617 Angle : 0.798 15.524 6471 Z= 0.381 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 Details of bonding type rmsd hydrogen bonds : bond 0.12346 ( 319) hydrogen bonds : angle 5.08480 ( 927) SS BOND : bond 0.00480 ( 17) SS BOND : angle 2.02817 ( 34) covalent geometry : bond 0.01245 ( 4766) covalent geometry : angle 0.78636 ( 6437) *********************** 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 : 0.593 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: 0.1482 time to fit residues: 11.1918 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 : 0.526 ------------------------------------------------------------------------------- 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 4783 Z= 0.149 Angle : 0.632 7.622 6471 Z= 0.318 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 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 319) hydrogen bonds : angle 4.10972 ( 927) SS BOND : bond 0.00485 ( 17) SS BOND : angle 1.94757 ( 34) covalent geometry : bond 0.00352 ( 4766) covalent geometry : angle 0.61740 ( 6437) *********************** 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 : 0.581 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: 0.1269 time to fit residues: 8.9693 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 : 0.617 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.122005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095824 restraints weight = 7966.623| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.84 r_work: 0.3094 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4783 Z= 0.158 Angle : 0.602 7.640 6471 Z= 0.307 Chirality : 0.042 0.179 716 Planarity : 0.004 0.033 832 Dihedral : 5.623 43.456 699 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.25 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 0.013 0.002 PHE A 554 TYR 0.018 0.002 TYR A 150 ARG 0.005 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 319) hydrogen bonds : angle 4.01698 ( 927) SS BOND : bond 0.00511 ( 17) SS BOND : angle 1.76721 ( 34) covalent geometry : bond 0.00376 ( 4766) covalent geometry : angle 0.58972 ( 6437) *********************** 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 : 0.567 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.1091 time to fit residues: 9.3503 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 : 0.570 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.123479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097494 restraints weight = 7891.855| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.84 r_work: 0.3115 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4783 Z= 0.131 Angle : 0.565 6.848 6471 Z= 0.291 Chirality : 0.040 0.169 716 Planarity : 0.003 0.032 832 Dihedral : 4.921 28.739 699 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.57 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: 1.77 (0.37), residues: 579 helix: 1.69 (0.26), residues: 409 sheet: None (None), residues: 0 loop : 0.01 (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 0.015 0.001 TYR A 161 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 319) hydrogen bonds : angle 3.91079 ( 927) SS BOND : bond 0.00454 ( 17) SS BOND : angle 1.92940 ( 34) covalent geometry : bond 0.00305 ( 4766) covalent geometry : angle 0.54881 ( 6437) *********************** 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 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.593 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.1180 time to fit residues: 9.8405 Evaluate side-chains 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.121583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095432 restraints weight = 8024.892| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.84 r_work: 0.3082 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4783 Z= 0.148 Angle : 0.581 8.050 6471 Z= 0.296 Chirality : 0.040 0.161 716 Planarity : 0.004 0.032 832 Dihedral : 4.625 22.308 699 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.76 % Allowed : 18.31 % 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: 1.71 (0.37), residues: 579 helix: 1.66 (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 0.002 PHE A 554 TYR 0.016 0.002 TYR A 161 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 319) hydrogen bonds : angle 3.94053 ( 927) SS BOND : bond 0.00475 ( 17) SS BOND : angle 1.83886 ( 34) covalent geometry : bond 0.00351 ( 4766) covalent geometry : angle 0.56742 ( 6437) *********************** 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 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7738 (pm20) outliers start: 14 outliers final: 11 residues processed: 56 average time/residue: 0.1122 time to fit residues: 9.5264 Evaluate side-chains 51 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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: 0.6980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.122834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.097839 restraints weight = 7907.200| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.76 r_work: 0.3123 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4783 Z= 0.129 Angle : 0.564 7.942 6471 Z= 0.288 Chirality : 0.039 0.152 716 Planarity : 0.003 0.032 832 Dihedral : 4.466 22.826 699 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.76 % Allowed : 19.09 % 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: 1.64 (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 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE A 554 TYR 0.014 0.001 TYR A 161 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 319) hydrogen bonds : angle 3.89468 ( 927) SS BOND : bond 0.00430 ( 17) SS BOND : angle 1.91617 ( 34) covalent geometry : bond 0.00304 ( 4766) covalent geometry : angle 0.54820 ( 6437) *********************** 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: 14 poor density : 49 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7675 (pm20) outliers start: 14 outliers final: 11 residues processed: 61 average time/residue: 0.1124 time to fit residues: 10.3320 Evaluate side-chains 55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 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 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: 0.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.122689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096686 restraints weight = 7972.206| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.85 r_work: 0.3108 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4783 Z= 0.133 Angle : 0.597 8.834 6471 Z= 0.298 Chirality : 0.040 0.183 716 Planarity : 0.003 0.031 832 Dihedral : 4.387 24.176 699 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.76 % Allowed : 18.90 % Favored : 78.35 % 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: 1.75 (0.37), residues: 579 helix: 1.60 (0.26), residues: 419 sheet: None (None), residues: 0 loop : 0.13 (0.54), residues: 160 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 0.001 TYR A 161 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 319) hydrogen bonds : angle 3.89724 ( 927) SS BOND : bond 0.00413 ( 17) SS BOND : angle 1.88167 ( 34) covalent geometry : bond 0.00310 ( 4766) covalent geometry : angle 0.58290 ( 6437) *********************** 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: 14 poor density : 44 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: A 551 PHE cc_start: 0.8346 (m-80) cc_final: 0.7689 (t80) outliers start: 14 outliers final: 10 residues processed: 56 average time/residue: 0.1203 time to fit residues: 9.6863 Evaluate side-chains 52 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 49 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.122858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097397 restraints weight = 7888.566| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.76 r_work: 0.3117 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4783 Z= 0.126 Angle : 0.575 7.863 6471 Z= 0.290 Chirality : 0.040 0.181 716 Planarity : 0.003 0.029 832 Dihedral : 4.305 24.404 699 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.56 % Allowed : 19.69 % 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: 1.79 (0.37), residues: 579 helix: 1.70 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.02 (0.54), residues: 165 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 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 319) hydrogen bonds : angle 3.86588 ( 927) SS BOND : bond 0.00410 ( 17) SS BOND : angle 1.80758 ( 34) covalent geometry : bond 0.00291 ( 4766) covalent geometry : angle 0.56114 ( 6437) *********************** 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: 13 poor density : 45 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: A 551 PHE cc_start: 0.8309 (m-80) cc_final: 0.7707 (t80) outliers start: 13 outliers final: 12 residues processed: 56 average time/residue: 0.1239 time to fit residues: 10.0113 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 : 0.570 ------------------------------------------------------------------------------- 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 128 HIS 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 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: 0.9980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097903 restraints weight = 7920.970| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.75 r_work: 0.3139 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4783 Z= 0.122 Angle : 0.570 7.771 6471 Z= 0.288 Chirality : 0.039 0.172 716 Planarity : 0.003 0.029 832 Dihedral : 4.280 24.747 699 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.15 % Allowed : 19.09 % 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: 1.80 (0.37), residues: 579 helix: 1.72 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.03 (0.54), residues: 165 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 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 319) hydrogen bonds : angle 3.82286 ( 927) SS BOND : bond 0.00408 ( 17) SS BOND : angle 1.74016 ( 34) covalent geometry : bond 0.00280 ( 4766) covalent geometry : angle 0.55707 ( 6437) *********************** 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 : 0.580 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: A 551 PHE cc_start: 0.8307 (m-80) cc_final: 0.7736 (t80) outliers start: 16 outliers final: 14 residues processed: 58 average time/residue: 0.1210 time to fit residues: 10.2099 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 : 0.526 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 3 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.124553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099214 restraints weight = 7905.683| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.75 r_work: 0.3163 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4783 Z= 0.113 Angle : 0.565 7.710 6471 Z= 0.286 Chirality : 0.038 0.180 716 Planarity : 0.003 0.029 832 Dihedral : 4.292 25.214 699 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.95 % Allowed : 19.49 % 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: 1.84 (0.36), residues: 579 helix: 1.72 (0.26), residues: 414 sheet: None (None), residues: 0 loop : 0.06 (0.53), 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 0.013 0.002 TYR A 140 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 319) hydrogen bonds : angle 3.81780 ( 927) SS BOND : bond 0.00380 ( 17) SS BOND : angle 1.65621 ( 34) covalent geometry : bond 0.00251 ( 4766) covalent geometry : angle 0.55390 ( 6437) ********************** 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 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7632 (pm20) outliers start: 15 outliers final: 14 residues processed: 54 average time/residue: 0.1199 time to fit residues: 9.3724 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 : 0.529 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.0060 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.123138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097722 restraints weight = 7937.342| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.74 r_work: 0.3135 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4783 Z= 0.128 Angle : 0.580 7.633 6471 Z= 0.292 Chirality : 0.040 0.172 716 Planarity : 0.003 0.029 832 Dihedral : 4.315 25.770 699 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: 1.76 (0.36), residues: 579 helix: 1.56 (0.26), residues: 423 sheet: None (None), residues: 0 loop : 0.26 (0.55), residues: 156 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 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 319) hydrogen bonds : angle 3.82426 ( 927) SS BOND : bond 0.00421 ( 17) SS BOND : angle 1.73735 ( 34) covalent geometry : bond 0.00297 ( 4766) covalent geometry : angle 0.56769 ( 6437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.16 seconds wall clock time: 43 minutes 10.03 seconds (2590.03 seconds total)