Starting phenix.real_space_refine on Sun Apr 27 05:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vaf_43090/04_2025/8vaf_43090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vaf_43090/04_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_43090/04_2025/8vaf_43090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vaf_43090/04_2025/8vaf_43090.map" model { file = "/net/cci-nas-00/data/ceres_data/8vaf_43090/04_2025/8vaf_43090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vaf_43090/04_2025/8vaf_43090.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.77, per 1000 atoms: 1.03 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: 1.07 Conformation dependent library (CDL) restraints added in 511.9 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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: 1.27 Time building geometry restraints manager: 1.28 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: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (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 TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 PHE 0.021 0.001 PHE A 165 TYR 0.024 0.002 TYR A 161 ARG 0.002 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.10743 ( 310) hydrogen bonds : angle 4.44629 ( 924) SS BOND : bond 0.17806 ( 17) SS BOND : angle 10.22339 ( 34) covalent geometry : bond 0.00296 ( 4713) covalent geometry : angle 0.58669 ( 6357) *********************** 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 : 0.582 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1380 time to fit residues: 8.9472 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 : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 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 = 0.3636 r_free = 0.3636 target = 0.128253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101588 restraints weight = 7277.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104015 restraints weight = 5096.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105624 restraints weight = 4015.337| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4730 Z= 0.134 Angle : 0.550 6.531 6391 Z= 0.286 Chirality : 0.039 0.158 706 Planarity : 0.004 0.046 828 Dihedral : 4.251 25.988 622 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.59 % Allowed : 8.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (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 TRP 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.011 0.001 PHE A 165 TYR 0.019 0.002 TYR A 161 ARG 0.002 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 310) hydrogen bonds : angle 3.80123 ( 924) SS BOND : bond 0.00456 ( 17) SS BOND : angle 1.67167 ( 34) covalent geometry : bond 0.00311 ( 4713) covalent geometry : angle 0.53725 ( 6357) *********************** 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 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.534 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.1314 time to fit residues: 6.8986 Evaluate side-chains 23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.125990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098042 restraints weight = 7356.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100830 restraints weight = 4823.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102731 restraints weight = 3677.353| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1504 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= 0.146 Angle : 0.548 6.140 6391 Z= 0.286 Chirality : 0.039 0.158 706 Planarity : 0.004 0.042 828 Dihedral : 4.275 26.689 622 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.18 % Allowed : 12.01 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.36), residues: 579 helix: 1.72 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.29 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 PHE 0.010 0.001 PHE A 554 TYR 0.016 0.001 TYR A 370 ARG 0.002 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 310) hydrogen bonds : angle 3.82749 ( 924) SS BOND : bond 0.00348 ( 17) SS BOND : angle 1.62372 ( 34) covalent geometry : bond 0.00347 ( 4713) covalent geometry : angle 0.53643 ( 6357) *********************** 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 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.506 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.1466 time to fit residues: 8.0385 Evaluate side-chains 25 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.126896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099222 restraints weight = 7445.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101968 restraints weight = 4921.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103963 restraints weight = 3762.684| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4730 Z= 0.124 Angle : 0.519 5.990 6391 Z= 0.273 Chirality : 0.038 0.154 706 Planarity : 0.004 0.051 828 Dihedral : 4.166 21.980 622 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.57 % Allowed : 13.39 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.36), residues: 579 helix: 1.71 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.25 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 9 PHE 0.010 0.001 PHE A 554 TYR 0.015 0.001 TYR A 370 ARG 0.001 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 310) hydrogen bonds : angle 3.70566 ( 924) SS BOND : bond 0.00400 ( 17) SS BOND : angle 1.51536 ( 34) covalent geometry : bond 0.00286 ( 4713) covalent geometry : angle 0.50867 ( 6357) *********************** 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 36 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.503 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.1210 time to fit residues: 6.2301 Evaluate side-chains 30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 480 SER 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 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.127070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099901 restraints weight = 7459.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102632 restraints weight = 4949.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104496 restraints weight = 3788.368| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1809 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 : 0.506 6.601 6391 Z= 0.267 Chirality : 0.037 0.155 706 Planarity : 0.003 0.030 828 Dihedral : 4.057 24.383 622 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.57 % Allowed : 14.57 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.36), residues: 579 helix: 1.77 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.28 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 67 PHE 0.009 0.001 PHE A 554 TYR 0.012 0.001 TYR A 370 ARG 0.001 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 310) hydrogen bonds : angle 3.61634 ( 924) SS BOND : bond 0.00331 ( 17) SS BOND : angle 1.67945 ( 34) covalent geometry : bond 0.00266 ( 4713) covalent geometry : angle 0.49266 ( 6357) *********************** 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 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.728 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.1420 time to fit residues: 7.1392 Evaluate side-chains 30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 177 CYS 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 23 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.125084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097488 restraints weight = 7496.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100247 restraints weight = 4933.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102209 restraints weight = 3762.692| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1996 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= 0.138 Angle : 0.526 5.871 6391 Z= 0.278 Chirality : 0.039 0.156 706 Planarity : 0.003 0.031 828 Dihedral : 4.117 22.791 622 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.77 % Allowed : 15.35 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.36), residues: 579 helix: 1.71 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -1.37 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.004 0.001 HIS A 67 PHE 0.009 0.001 PHE A 554 TYR 0.012 0.001 TYR A 411 ARG 0.002 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 310) hydrogen bonds : angle 3.70645 ( 924) SS BOND : bond 0.00340 ( 17) SS BOND : angle 1.60874 ( 34) covalent geometry : bond 0.00328 ( 4713) covalent geometry : angle 0.51381 ( 6357) *********************** 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 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.519 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.1448 time to fit residues: 7.0960 Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.0050 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.126822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099289 restraints weight = 7466.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102145 restraints weight = 4915.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104082 restraints weight = 3733.400| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4730 Z= 0.112 Angle : 0.499 6.217 6391 Z= 0.264 Chirality : 0.037 0.148 706 Planarity : 0.003 0.029 828 Dihedral : 3.964 21.696 622 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.36 % Allowed : 15.94 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.36), residues: 579 helix: 1.80 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.39 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 67 PHE 0.009 0.001 PHE A 554 TYR 0.009 0.001 TYR A 370 ARG 0.001 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 310) hydrogen bonds : angle 3.63330 ( 924) SS BOND : bond 0.00427 ( 17) SS BOND : angle 1.58494 ( 34) covalent geometry : bond 0.00255 ( 4713) covalent geometry : angle 0.48721 ( 6357) *********************** 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 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.507 Fit side-chains REVERT: A 548 MET cc_start: 0.7471 (tpp) cc_final: 0.7208 (tpp) outliers start: 12 outliers final: 6 residues processed: 43 average time/residue: 0.1388 time to fit residues: 8.3940 Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.0000 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.127167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099090 restraints weight = 7407.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102170 restraints weight = 4681.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104378 restraints weight = 3461.862| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4730 Z= 0.115 Angle : 0.525 6.453 6391 Z= 0.279 Chirality : 0.037 0.144 706 Planarity : 0.003 0.032 828 Dihedral : 3.950 21.048 622 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.18 % Allowed : 17.91 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.36), residues: 579 helix: 1.82 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.42 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.006 0.001 HIS A 67 PHE 0.013 0.001 PHE A 554 TYR 0.009 0.001 TYR A 370 ARG 0.001 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 310) hydrogen bonds : angle 3.65519 ( 924) SS BOND : bond 0.00428 ( 17) SS BOND : angle 1.67484 ( 34) covalent geometry : bond 0.00265 ( 4713) covalent geometry : angle 0.51162 ( 6357) *********************** 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 38 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7554 (tpp) cc_final: 0.7321 (tpp) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.1449 time to fit residues: 7.2311 Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.0020 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.127882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100775 restraints weight = 7512.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103795 restraints weight = 4748.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105843 restraints weight = 3540.420| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 0.040 4730 Z= 0.128 Angle : 0.521 5.808 6391 Z= 0.275 Chirality : 0.038 0.149 706 Planarity : 0.004 0.041 828 Dihedral : 3.997 21.345 622 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.36), residues: 579 helix: 1.80 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.37 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.005 0.001 HIS A 67 PHE 0.012 0.001 PHE A 554 TYR 0.010 0.001 TYR A 411 ARG 0.002 0.000 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 310) hydrogen bonds : angle 3.72652 ( 924) SS BOND : bond 0.00428 ( 17) SS BOND : angle 1.54960 ( 34) covalent geometry : bond 0.00302 ( 4713) covalent geometry : angle 0.50982 ( 6357) *********************** 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 38 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7488 (tpp) cc_final: 0.7227 (tpp) outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.1257 time to fit residues: 6.4889 Evaluate side-chains 34 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.129303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102367 restraints weight = 7419.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105413 restraints weight = 4705.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107461 restraints weight = 3511.836| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2250 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= 0.110 Angle : 0.502 5.349 6391 Z= 0.265 Chirality : 0.037 0.144 706 Planarity : 0.004 0.044 828 Dihedral : 3.891 20.525 622 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.18 % Allowed : 18.90 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.36), residues: 579 helix: 1.87 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.42 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.006 0.001 HIS A 67 PHE 0.013 0.001 PHE A 554 TYR 0.010 0.001 TYR A 161 ARG 0.001 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 310) hydrogen bonds : angle 3.69571 ( 924) SS BOND : bond 0.00384 ( 17) SS BOND : angle 1.37221 ( 34) covalent geometry : bond 0.00251 ( 4713) covalent geometry : angle 0.49277 ( 6357) ********************** 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 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.551 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.1363 time to fit residues: 6.4885 Evaluate side-chains 33 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100578 restraints weight = 7502.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103559 restraints weight = 4749.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105620 restraints weight = 3540.299| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2310 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= 0.127 Angle : 0.528 7.298 6391 Z= 0.275 Chirality : 0.038 0.149 706 Planarity : 0.004 0.048 828 Dihedral : 3.968 21.434 622 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.38 % Allowed : 18.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.36), residues: 579 helix: 1.83 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.36 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.006 0.001 HIS A 67 PHE 0.053 0.001 PHE A 568 TYR 0.011 0.001 TYR A 411 ARG 0.002 0.000 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 310) hydrogen bonds : angle 3.73265 ( 924) SS BOND : bond 0.00389 ( 17) SS BOND : angle 1.36615 ( 34) covalent geometry : bond 0.00298 ( 4713) covalent geometry : angle 0.52017 ( 6357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.97 seconds wall clock time: 35 minutes 24.07 seconds (2124.07 seconds total)