Starting phenix.real_space_refine on Wed Sep 17 04:58:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vaf_43090/09_2025/8vaf_43090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vaf_43090/09_2025/8vaf_43090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vaf_43090/09_2025/8vaf_43090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vaf_43090/09_2025/8vaf_43090.map" model { file = "/net/cci-nas-00/data/ceres_data/8vaf_43090/09_2025/8vaf_43090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vaf_43090/09_2025/8vaf_43090.cif" } resolution = 3.5 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= 0.008 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 41 5.16 5 C 2918 2.51 5 N 782 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 4623 Number of models: 1 Model: "" Number of chains: 1 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} Time building chain proxies: 1.39, per 1000 atoms: 0.30 Number of scatterers: 4623 At special positions: 0 Unit cell: (66.7, 90.85, 93.725, 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 41 16.00 O 882 8.00 N 782 7.00 C 2918 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=2.03 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=2.04 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=1.30 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=2.04 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: 0.40 Conformation dependent library (CDL) restraints added in 198.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 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 59 through 64 removed outlier: 3.754A pdb=" N ASP A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 64' Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.661A pdb=" N CYS A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.768A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.666A pdb=" N ARG A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 179 through 223 removed outlier: 7.121A pdb=" N GLU A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ARG A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.174A 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 250 through 267 Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.955A pdb=" N LYS A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 277' Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 322 through 338 Processing helix chain 'A' and resid 342 through 360 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.682A pdb=" N CYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 397 removed outlier: 4.392A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.958A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 415 Processing helix chain 'A' and resid 419 through 438 removed outlier: 3.911A pdb=" N GLY A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.985A pdb=" N CYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.522A pdb=" N CYS A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.846A pdb=" N PHE A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 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 581 removed outlier: 4.119A pdb=" N CYS A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 924 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: 0.71 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1530 1.35 - 1.47: 1034 1.47 - 1.60: 2102 1.60 - 1.72: 0 1.72 - 1.84: 47 Bond restraints: 4713 Sorted by residual: bond pdb=" N ARG A 160 " pdb=" CA ARG A 160 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.90e+00 bond pdb=" N CYS A 361 " pdb=" CA CYS A 361 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.63e+00 bond pdb=" N CYS A 360 " pdb=" CA CYS A 360 " ideal model delta sigma weight residual 1.466 1.482 -0.015 1.36e-02 5.41e+03 1.25e+00 bond pdb=" C CYS A 360 " pdb=" O CYS A 360 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.22e-02 6.72e+03 1.22e+00 bond pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.13e+00 ... (remaining 4708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 6206 1.65 - 3.30: 116 3.30 - 4.96: 28 4.96 - 6.61: 6 6.61 - 8.26: 1 Bond angle restraints: 6357 Sorted by residual: angle pdb=" CA CYS A 289 " pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " ideal model delta sigma weight residual 114.40 122.66 -8.26 2.30e+00 1.89e-01 1.29e+01 angle pdb=" C ALA A 553 " pdb=" N PHE A 554 " pdb=" CA PHE A 554 " ideal model delta sigma weight residual 120.68 114.90 5.78 1.70e+00 3.46e-01 1.15e+01 angle pdb=" C LYS A 359 " pdb=" N CYS A 360 " pdb=" CA CYS A 360 " ideal model delta sigma weight residual 122.76 117.30 5.46 1.63e+00 3.76e-01 1.12e+01 angle pdb=" N PHE A 554 " pdb=" CA PHE A 554 " pdb=" CB PHE A 554 " ideal model delta sigma weight residual 110.30 114.61 -4.31 1.54e+00 4.22e-01 7.83e+00 angle pdb=" C VAL A 315 " pdb=" N CYS A 316 " pdb=" CA CYS A 316 " ideal model delta sigma weight residual 122.06 116.96 5.10 1.86e+00 2.89e-01 7.51e+00 ... (remaining 6352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 2563 16.63 - 33.26: 310 33.26 - 49.89: 79 49.89 - 66.52: 12 66.52 - 83.15: 15 Dihedral angle restraints: 2979 sinusoidal: 1241 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS A 514 " pdb=" SG CYS A 514 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual 93.00 176.15 -83.15 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 487 " pdb=" CB CYS A 487 " ideal model delta sinusoidal sigma weight residual -86.00 -163.71 77.71 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 91 " pdb=" CB CYS A 91 " ideal model delta sinusoidal sigma weight residual 93.00 169.24 -76.24 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 2976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 452 0.030 - 0.059: 165 0.059 - 0.089: 52 0.089 - 0.118: 30 0.118 - 0.148: 7 Chirality restraints: 706 Sorted by residual: chirality pdb=" CA ASP A 563 " pdb=" N ASP A 563 " pdb=" C ASP A 563 " pdb=" CB ASP A 563 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA CYS A 476 " pdb=" N CYS A 476 " pdb=" C CYS A 476 " pdb=" CB CYS A 476 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA CYS A 437 " pdb=" N CYS A 437 " pdb=" C CYS A 437 " pdb=" CB CYS A 437 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 703 not shown) Planarity restraints: 828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 359 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C LYS A 359 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS A 359 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS A 360 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 281 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 282 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 34 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 35 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.020 5.00e-02 4.00e+02 ... (remaining 825 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 625 2.75 - 3.29: 4686 3.29 - 3.83: 7676 3.83 - 4.36: 8291 4.36 - 4.90: 14729 Nonbonded interactions: 36007 Sorted by model distance: nonbonded pdb=" OE2 GLU A 230 " pdb=" OH TYR A 263 " model vdw 2.216 3.040 nonbonded pdb=" O CYS A 34 " pdb=" OH TYR A 140 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU A 141 " pdb=" NH1 ARG A 145 " model vdw 2.327 3.120 nonbonded pdb=" OD2 ASP A 550 " pdb=" NZ LYS A 574 " model vdw 2.333 3.120 nonbonded pdb=" O LEU A 408 " pdb=" OG1 THR A 412 " model vdw 2.336 3.040 ... (remaining 36002 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.030 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: 0.010 Set scattering table: 0.020 Process input model: 6.520 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.011 0.734 4730 Z= 0.552 Angle : 0.948 58.244 6391 Z= 0.476 Chirality : 0.040 0.148 706 Planarity : 0.004 0.037 828 Dihedral : 15.266 82.545 1788 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.47 (0.36), residues: 579 helix: 1.75 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -1.01 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.024 0.002 TYR A 161 PHE 0.021 0.001 PHE A 165 TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4713) covalent geometry : angle 0.58669 ( 6357) SS BOND : bond 0.17806 ( 17) SS BOND : angle 10.22339 ( 34) hydrogen bonds : bond 0.10743 ( 310) hydrogen bonds : angle 4.44629 ( 924) *********************** 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 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.146 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0651 time to fit residues: 4.2527 Evaluate side-chains 26 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101416 restraints weight = 7362.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103873 restraints weight = 5142.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105562 restraints weight = 4047.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106775 restraints weight = 3453.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107363 restraints weight = 3095.268| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4730 Z= 0.135 Angle : 0.550 6.600 6391 Z= 0.286 Chirality : 0.039 0.158 706 Planarity : 0.004 0.046 828 Dihedral : 4.256 26.236 622 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.79 % Allowed : 8.27 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.36), residues: 579 helix: 1.81 (0.26), residues: 423 sheet: None (None), residues: 0 loop : -1.25 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.019 0.002 TYR A 161 PHE 0.011 0.001 PHE A 165 TRP 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4713) covalent geometry : angle 0.53642 ( 6357) SS BOND : bond 0.00451 ( 17) SS BOND : angle 1.72289 ( 34) hydrogen bonds : bond 0.03957 ( 310) hydrogen bonds : angle 3.80494 ( 924) *********************** 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 38 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.189 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 37 average time/residue: 0.0618 time to fit residues: 3.3524 Evaluate side-chains 26 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 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 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099122 restraints weight = 7385.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101941 restraints weight = 4856.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103925 restraints weight = 3692.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105268 restraints weight = 3071.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106055 restraints weight = 2718.057| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4730 Z= 0.130 Angle : 0.534 6.131 6391 Z= 0.279 Chirality : 0.038 0.153 706 Planarity : 0.004 0.042 828 Dihedral : 4.204 25.872 622 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.18 % Allowed : 11.61 % Favored : 87.20 % 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: 1.51 (0.36), residues: 579 helix: 1.74 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -1.26 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.016 0.001 TYR A 370 PHE 0.009 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4713) covalent geometry : angle 0.52237 ( 6357) SS BOND : bond 0.00371 ( 17) SS BOND : angle 1.62648 ( 34) hydrogen bonds : bond 0.03874 ( 310) hydrogen bonds : angle 3.74037 ( 924) *********************** 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 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.223 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 36 average time/residue: 0.0584 time to fit residues: 3.0828 Evaluate side-chains 26 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS 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 44 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN 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 = 0.127953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100265 restraints weight = 7456.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103067 restraints weight = 4957.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105041 restraints weight = 3777.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106217 restraints weight = 3145.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106884 restraints weight = 2799.450| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4730 Z= 0.116 Angle : 0.502 5.861 6391 Z= 0.264 Chirality : 0.038 0.150 706 Planarity : 0.004 0.044 828 Dihedral : 4.073 21.806 622 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.38 % Allowed : 12.99 % Favored : 85.63 % 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: 1.59 (0.36), residues: 579 helix: 1.82 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.29 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 348 TYR 0.015 0.001 TYR A 370 PHE 0.009 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4713) covalent geometry : angle 0.49146 ( 6357) SS BOND : bond 0.00316 ( 17) SS BOND : angle 1.49368 ( 34) hydrogen bonds : bond 0.03582 ( 310) hydrogen bonds : angle 3.67989 ( 924) *********************** 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 39 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.202 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.0702 time to fit residues: 3.6772 Evaluate side-chains 31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 169 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 11 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098739 restraints weight = 7412.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101190 restraints weight = 5203.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102669 restraints weight = 4102.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103982 restraints weight = 3526.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104626 restraints weight = 3152.386| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4730 Z= 0.145 Angle : 0.532 6.526 6391 Z= 0.280 Chirality : 0.039 0.156 706 Planarity : 0.004 0.047 828 Dihedral : 4.082 22.856 622 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.17 % Allowed : 14.17 % Favored : 83.66 % 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: 1.54 (0.36), residues: 579 helix: 1.75 (0.26), residues: 434 sheet: None (None), residues: 0 loop : -1.23 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.012 0.001 TYR A 411 PHE 0.010 0.001 PHE A 554 TRP 0.003 0.001 TRP A 214 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4713) covalent geometry : angle 0.51904 ( 6357) SS BOND : bond 0.00372 ( 17) SS BOND : angle 1.68805 ( 34) hydrogen bonds : bond 0.03918 ( 310) hydrogen bonds : angle 3.73209 ( 924) *********************** 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 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.193 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 34 average time/residue: 0.0566 time to fit residues: 2.9106 Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.0010 chunk 46 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.098895 restraints weight = 7562.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101751 restraints weight = 4938.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103651 restraints weight = 3729.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105094 restraints weight = 3105.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105973 restraints weight = 2731.406| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4730 Z= 0.118 Angle : 0.507 6.482 6391 Z= 0.267 Chirality : 0.038 0.151 706 Planarity : 0.004 0.046 828 Dihedral : 3.992 21.722 622 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.97 % Allowed : 15.94 % Favored : 82.09 % 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: 1.59 (0.36), residues: 579 helix: 1.81 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.27 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 348 TYR 0.011 0.001 TYR A 370 PHE 0.009 0.001 PHE A 554 TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4713) covalent geometry : angle 0.49325 ( 6357) SS BOND : bond 0.00367 ( 17) SS BOND : angle 1.65359 ( 34) hydrogen bonds : bond 0.03576 ( 310) hydrogen bonds : angle 3.64694 ( 924) *********************** 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 41 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.171 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 37 average time/residue: 0.0667 time to fit residues: 3.3939 Evaluate side-chains 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 chunk 36 optimal weight: 0.0010 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 0.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099392 restraints weight = 7506.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102586 restraints weight = 4685.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104808 restraints weight = 3429.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106366 restraints weight = 2787.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107107 restraints weight = 2413.856| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4730 Z= 0.107 Angle : 0.501 6.110 6391 Z= 0.264 Chirality : 0.037 0.143 706 Planarity : 0.004 0.047 828 Dihedral : 3.922 20.264 622 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.77 % Allowed : 16.93 % Favored : 81.30 % 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: 1.59 (0.36), residues: 579 helix: 1.84 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.34 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.010 0.001 TYR A 370 PHE 0.010 0.001 PHE A 554 TRP 0.001 0.001 TRP A 214 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4713) covalent geometry : angle 0.48349 ( 6357) SS BOND : bond 0.00388 ( 17) SS BOND : angle 1.87503 ( 34) hydrogen bonds : bond 0.03239 ( 310) hydrogen bonds : angle 3.64093 ( 924) *********************** 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 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7512 (tpp) cc_final: 0.7265 (tpp) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.0694 time to fit residues: 3.8831 Evaluate side-chains 31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098397 restraints weight = 7507.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101228 restraints weight = 4873.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103243 restraints weight = 3673.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104676 restraints weight = 3035.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105263 restraints weight = 2669.839| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4730 Z= 0.137 Angle : 0.536 6.065 6391 Z= 0.283 Chirality : 0.038 0.152 706 Planarity : 0.004 0.046 828 Dihedral : 3.978 22.238 622 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.77 % Allowed : 17.72 % Favored : 80.51 % 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: 1.54 (0.36), residues: 579 helix: 1.81 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -1.42 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.011 0.001 TYR A 411 PHE 0.009 0.001 PHE A 554 TRP 0.003 0.001 TRP A 214 HIS 0.007 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4713) covalent geometry : angle 0.52583 ( 6357) SS BOND : bond 0.00469 ( 17) SS BOND : angle 1.51326 ( 34) hydrogen bonds : bond 0.03782 ( 310) hydrogen bonds : angle 3.71837 ( 924) *********************** 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 39 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7451 (tpp) cc_final: 0.7159 (tpp) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.0610 time to fit residues: 3.2129 Evaluate side-chains 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098104 restraints weight = 7423.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100933 restraints weight = 4882.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102773 restraints weight = 3684.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104215 restraints weight = 3082.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105009 restraints weight = 2705.700| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4730 Z= 0.134 Angle : 0.522 5.485 6391 Z= 0.277 Chirality : 0.038 0.153 706 Planarity : 0.004 0.047 828 Dihedral : 3.989 22.485 622 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.57 % Allowed : 17.91 % Favored : 80.51 % 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: 1.56 (0.36), residues: 579 helix: 1.82 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -1.41 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 348 TYR 0.011 0.001 TYR A 411 PHE 0.009 0.001 PHE A 554 TRP 0.003 0.001 TRP A 214 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4713) covalent geometry : angle 0.51285 ( 6357) SS BOND : bond 0.00390 ( 17) SS BOND : angle 1.44105 ( 34) hydrogen bonds : bond 0.03744 ( 310) hydrogen bonds : angle 3.72861 ( 924) *********************** 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 39 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7451 (tpp) cc_final: 0.7179 (tpp) outliers start: 8 outliers final: 8 residues processed: 35 average time/residue: 0.0647 time to fit residues: 3.2447 Evaluate side-chains 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.0570 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102418 restraints weight = 7490.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105287 restraints weight = 4849.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107243 restraints weight = 3657.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108621 restraints weight = 3044.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109170 restraints weight = 2677.083| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4730 Z= 0.113 Angle : 0.495 5.391 6391 Z= 0.263 Chirality : 0.037 0.146 706 Planarity : 0.004 0.047 828 Dihedral : 3.896 21.313 622 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.77 % Allowed : 18.11 % Favored : 80.12 % 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 (0.36), residues: 579 helix: 1.98 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.011 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 67 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4713) covalent geometry : angle 0.48715 ( 6357) SS BOND : bond 0.00364 ( 17) SS BOND : angle 1.31010 ( 34) hydrogen bonds : bond 0.03416 ( 310) hydrogen bonds : angle 3.65113 ( 924) ********************** 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 41 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7484 (tpp) cc_final: 0.7209 (tpp) outliers start: 9 outliers final: 8 residues processed: 37 average time/residue: 0.0564 time to fit residues: 3.0774 Evaluate side-chains 39 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 554 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101860 restraints weight = 7478.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104867 restraints weight = 4759.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106858 restraints weight = 3558.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108258 restraints weight = 2946.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108931 restraints weight = 2588.177| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4730 Z= 0.114 Angle : 0.496 5.435 6391 Z= 0.263 Chirality : 0.037 0.146 706 Planarity : 0.004 0.048 828 Dihedral : 3.869 21.195 622 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.77 % Allowed : 17.91 % Favored : 80.31 % 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 (0.36), residues: 579 helix: 1.94 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.39 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.010 0.001 TYR A 161 PHE 0.052 0.001 PHE A 568 TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4713) covalent geometry : angle 0.48890 ( 6357) SS BOND : bond 0.00339 ( 17) SS BOND : angle 1.27773 ( 34) hydrogen bonds : bond 0.03442 ( 310) hydrogen bonds : angle 3.65874 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1102.35 seconds wall clock time: 19 minutes 45.30 seconds (1185.30 seconds total)