Starting phenix.real_space_refine on Wed Sep 17 05:00:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vac_43088/09_2025/8vac_43088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vac_43088/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vac_43088/09_2025/8vac_43088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vac_43088/09_2025/8vac_43088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vac_43088/09_2025/8vac_43088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vac_43088/09_2025/8vac_43088.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.18, per 1000 atoms: 0.25 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: 0.28 Conformation dependent library (CDL) restraints added in 160.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.12 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: 0.64 Time building geometry restraints manager: 0.35 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: 5.940 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: 0.140 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG A 98 TYR 0.014 0.002 TYR A 150 PHE 0.023 0.002 PHE A 502 TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.01245 ( 4766) covalent geometry : angle 0.78636 ( 6437) SS BOND : bond 0.00480 ( 17) SS BOND : angle 2.02817 ( 34) hydrogen bonds : bond 0.12346 ( 319) hydrogen bonds : angle 5.08480 ( 927) *********************** 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 : 0.150 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: 0.0612 time to fit residues: 4.6174 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 : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 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 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 = 0.3656 r_free = 0.3656 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098816 restraints weight = 7908.263| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.74 r_work: 0.3149 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4783 Z= 0.159 Angle : 0.642 7.903 6471 Z= 0.322 Chirality : 0.042 0.173 716 Planarity : 0.004 0.036 832 Dihedral : 6.231 50.245 699 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.18 % Allowed : 8.86 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.36), residues: 579 helix: 1.44 (0.26), residues: 415 sheet: None (None), residues: 0 loop : -0.20 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 98 TYR 0.019 0.002 TYR A 150 PHE 0.014 0.002 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4766) covalent geometry : angle 0.62774 ( 6437) SS BOND : bond 0.00504 ( 17) SS BOND : angle 1.94996 ( 34) hydrogen bonds : bond 0.03867 ( 319) hydrogen bonds : angle 4.12174 ( 927) *********************** 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 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.127 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.0452 time to fit residues: 3.2307 Evaluate side-chains 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 128 HIS 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 54 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.123925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097970 restraints weight = 7854.928| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.82 r_work: 0.3129 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4783 Z= 0.131 Angle : 0.572 6.729 6471 Z= 0.291 Chirality : 0.040 0.169 716 Planarity : 0.004 0.033 832 Dihedral : 5.570 43.228 699 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.97 % Allowed : 13.19 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.37), residues: 579 helix: 1.66 (0.26), residues: 411 sheet: None (None), residues: 0 loop : 0.06 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.014 0.001 TYR A 150 PHE 0.013 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4766) covalent geometry : angle 0.56054 ( 6437) SS BOND : bond 0.00445 ( 17) SS BOND : angle 1.64736 ( 34) hydrogen bonds : bond 0.03556 ( 319) hydrogen bonds : angle 3.94412 ( 927) *********************** 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 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.149 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 0.0383 time to fit residues: 3.4978 Evaluate side-chains 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097008 restraints weight = 8011.259| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.89 r_work: 0.3108 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4783 Z= 0.137 Angle : 0.573 7.480 6471 Z= 0.294 Chirality : 0.040 0.170 716 Planarity : 0.004 0.032 832 Dihedral : 4.962 29.990 699 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.36 % Allowed : 15.16 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.37), residues: 579 helix: 1.69 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.05 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.015 0.002 TYR A 161 PHE 0.013 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4766) covalent geometry : angle 0.55612 ( 6437) SS BOND : bond 0.00451 ( 17) SS BOND : angle 1.97330 ( 34) hydrogen bonds : bond 0.03598 ( 319) hydrogen bonds : angle 3.91760 ( 927) *********************** 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 58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.170 Fit side-chains REVERT: A 397 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7843 (pm20) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.0431 time to fit residues: 3.6773 Evaluate side-chains 49 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.122120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096110 restraints weight = 7978.731| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.84 r_work: 0.3097 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4783 Z= 0.140 Angle : 0.574 8.270 6471 Z= 0.292 Chirality : 0.040 0.159 716 Planarity : 0.004 0.031 832 Dihedral : 4.588 22.502 699 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.76 % Allowed : 17.72 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.37), residues: 579 helix: 1.69 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.07 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.016 0.002 TYR A 161 PHE 0.012 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4766) covalent geometry : angle 0.56035 ( 6437) SS BOND : bond 0.00481 ( 17) SS BOND : angle 1.80049 ( 34) hydrogen bonds : bond 0.03536 ( 319) hydrogen bonds : angle 3.90408 ( 927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.203 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 58 average time/residue: 0.0508 time to fit residues: 4.3480 Evaluate side-chains 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095894 restraints weight = 8024.876| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.77 r_work: 0.3093 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4783 Z= 0.160 Angle : 0.602 8.218 6471 Z= 0.307 Chirality : 0.040 0.159 716 Planarity : 0.004 0.034 832 Dihedral : 4.552 24.342 699 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.56 % Allowed : 19.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.37), residues: 579 helix: 1.59 (0.26), residues: 415 sheet: None (None), residues: 0 loop : -0.07 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.016 0.002 TYR A 161 PHE 0.012 0.002 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4766) covalent geometry : angle 0.58356 ( 6437) SS BOND : bond 0.00488 ( 17) SS BOND : angle 2.09441 ( 34) hydrogen bonds : bond 0.03668 ( 319) hydrogen bonds : angle 3.97233 ( 927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: A 551 PHE cc_start: 0.8367 (m-80) cc_final: 0.7669 (t80) outliers start: 13 outliers final: 11 residues processed: 59 average time/residue: 0.0533 time to fit residues: 4.5724 Evaluate side-chains 53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 0.0010 chunk 55 optimal weight: 7.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.122241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096263 restraints weight = 8006.557| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.81 r_work: 0.3103 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 0.032 4783 Z= 0.132 Angle : 0.569 7.900 6471 Z= 0.290 Chirality : 0.040 0.157 716 Planarity : 0.004 0.032 832 Dihedral : 4.392 24.153 699 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.37), residues: 579 helix: 1.64 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.09 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.015 0.001 TYR A 161 PHE 0.012 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4766) covalent geometry : angle 0.55726 ( 6437) SS BOND : bond 0.00435 ( 17) SS BOND : angle 1.70633 ( 34) hydrogen bonds : bond 0.03492 ( 319) hydrogen bonds : angle 3.88847 ( 927) *********************** 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 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7625 (pm20) outliers start: 14 outliers final: 11 residues processed: 58 average time/residue: 0.0507 time to fit residues: 4.3352 Evaluate side-chains 53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.0070 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.122765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096690 restraints weight = 8078.716| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.84 r_work: 0.3110 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4783 Z= 0.130 Angle : 0.587 8.951 6471 Z= 0.296 Chirality : 0.040 0.181 716 Planarity : 0.003 0.033 832 Dihedral : 4.356 24.756 699 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.95 % Allowed : 19.29 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.37), residues: 579 helix: 1.66 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.00 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.014 0.001 TYR A 161 PHE 0.013 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4766) covalent geometry : angle 0.57101 ( 6437) SS BOND : bond 0.00446 ( 17) SS BOND : angle 1.93716 ( 34) hydrogen bonds : bond 0.03520 ( 319) hydrogen bonds : angle 3.89275 ( 927) *********************** 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: 15 poor density : 45 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: A 551 PHE cc_start: 0.8334 (m-80) cc_final: 0.7672 (t80) outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.0501 time to fit residues: 4.2822 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.095938 restraints weight = 7890.439| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.79 r_work: 0.3098 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4783 Z= 0.144 Angle : 0.596 8.776 6471 Z= 0.301 Chirality : 0.040 0.189 716 Planarity : 0.003 0.032 832 Dihedral : 4.368 25.476 699 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.37), residues: 579 helix: 1.63 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.00 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.015 0.002 TYR A 161 PHE 0.012 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4766) covalent geometry : angle 0.58020 ( 6437) SS BOND : bond 0.00467 ( 17) SS BOND : angle 1.94147 ( 34) hydrogen bonds : bond 0.03611 ( 319) hydrogen bonds : angle 3.91229 ( 927) *********************** 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 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: A 551 PHE cc_start: 0.8330 (m-80) cc_final: 0.7701 (t80) outliers start: 16 outliers final: 15 residues processed: 57 average time/residue: 0.0514 time to fit residues: 4.2709 Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 496 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 559 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.122275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096309 restraints weight = 7961.735| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.80 r_work: 0.3104 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4783 Z= 0.135 Angle : 0.583 8.443 6471 Z= 0.295 Chirality : 0.040 0.181 716 Planarity : 0.003 0.033 832 Dihedral : 4.333 25.866 699 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.95 % Allowed : 19.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.37), residues: 579 helix: 1.64 (0.26), residues: 414 sheet: None (None), residues: 0 loop : 0.03 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.015 0.002 TYR A 161 PHE 0.012 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4766) covalent geometry : angle 0.56861 ( 6437) SS BOND : bond 0.00454 ( 17) SS BOND : angle 1.85501 ( 34) hydrogen bonds : bond 0.03522 ( 319) hydrogen bonds : angle 3.86577 ( 927) ********************** 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 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: A 551 PHE cc_start: 0.8327 (m-80) cc_final: 0.7724 (t80) outliers start: 15 outliers final: 14 residues processed: 57 average time/residue: 0.0555 time to fit residues: 4.4775 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 : 0.233 ------------------------------------------------------------------------------- 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 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097204 restraints weight = 8017.183| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.76 r_work: 0.3128 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4783 Z= 0.130 Angle : 0.585 8.786 6471 Z= 0.297 Chirality : 0.040 0.180 716 Planarity : 0.003 0.033 832 Dihedral : 4.351 25.947 699 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.15 % Allowed : 19.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.37), residues: 579 helix: 1.64 (0.26), residues: 414 sheet: None (None), residues: 0 loop : 0.01 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.015 0.002 TYR A 452 PHE 0.013 0.001 PHE A 507 TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4766) covalent geometry : angle 0.57219 ( 6437) SS BOND : bond 0.00431 ( 17) SS BOND : angle 1.77702 ( 34) hydrogen bonds : bond 0.03500 ( 319) hydrogen bonds : angle 3.86885 ( 927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1206.07 seconds wall clock time: 21 minutes 27.23 seconds (1287.23 seconds total)