Starting phenix.real_space_refine on Fri Aug 2 19:24:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vaf_43090/08_2024/8vaf_43090.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vaf_43090/08_2024/8vaf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vaf_43090/08_2024/8vaf_43090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vaf_43090/08_2024/8vaf_43090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vaf_43090/08_2024/8vaf_43090.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vaf_43090/08_2024/8vaf_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 Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 556": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.27, per 1000 atoms: 0.92 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 - 3.50 Amino acid : False - 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: 1.79 Conformation dependent library (CDL) restraints added in 968.3 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: 0.49 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: 1.22 Time building geometry restraints manager: 2.00 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: 100.00 - 106.80: 116 106.80 - 113.61: 2596 113.61 - 120.41: 1922 120.41 - 127.22: 1685 127.22 - 134.02: 38 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: 5.650 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- 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 : 0.003 0.035 4713 Z= 0.187 Angle : 0.587 8.259 6357 Z= 0.318 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.534 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1404 time to fit residues: 9.0614 Evaluate side-chains 26 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 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: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4713 Z= 0.190 Angle : 0.532 6.797 6357 Z= 0.278 Chirality : 0.039 0.156 706 Planarity : 0.004 0.045 828 Dihedral : 4.229 25.844 622 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.80 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: 1.53 (0.36), residues: 579 helix: 1.81 (0.26), residues: 423 sheet: None (None), residues: 0 loop : -1.24 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.010 0.001 PHE A 165 TYR 0.020 0.002 TYR A 161 ARG 0.002 0.000 ARG A 160 *********************** 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 36 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.570 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 0.1363 time to fit residues: 6.9623 Evaluate side-chains 24 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4713 Z= 0.199 Angle : 0.523 6.059 6357 Z= 0.275 Chirality : 0.039 0.154 706 Planarity : 0.004 0.044 828 Dihedral : 4.204 26.007 622 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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 (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: 1.51 (0.36), residues: 579 helix: 1.74 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -1.27 (0.50), residues: 146 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 0.009 0.001 PHE A 554 TYR 0.016 0.001 TYR A 370 ARG 0.002 0.000 ARG A 348 *********************** 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 38 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.541 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1364 time to fit residues: 7.3318 Evaluate side-chains 28 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4713 Z= 0.173 Angle : 0.495 5.891 6357 Z= 0.262 Chirality : 0.038 0.150 706 Planarity : 0.004 0.052 828 Dihedral : 4.115 21.545 622 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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 (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: 1.57 (0.36), residues: 579 helix: 1.82 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.31 (0.50), residues: 148 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 0.010 0.001 PHE A 554 TYR 0.015 0.001 TYR A 370 ARG 0.001 0.000 ARG A 348 *********************** 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 40 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.556 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.1493 time to fit residues: 8.2276 Evaluate side-chains 30 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4713 Z= 0.247 Angle : 0.547 5.930 6357 Z= 0.288 Chirality : 0.040 0.163 706 Planarity : 0.004 0.034 828 Dihedral : 4.242 23.756 622 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.97 % Allowed : 14.37 % 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 (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: 1.49 (0.36), residues: 579 helix: 1.70 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -1.26 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 214 HIS 0.004 0.001 HIS A 67 PHE 0.010 0.001 PHE A 554 TYR 0.014 0.001 TYR A 411 ARG 0.003 0.000 ARG A 348 *********************** 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 34 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.551 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 32 average time/residue: 0.1259 time to fit residues: 6.1467 Evaluate side-chains 30 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 554 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4713 Z= 0.214 Angle : 0.521 5.907 6357 Z= 0.277 Chirality : 0.039 0.162 706 Planarity : 0.004 0.034 828 Dihedral : 4.189 23.243 622 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.77 % Allowed : 15.75 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.36), residues: 579 helix: 1.70 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -1.41 (0.50), residues: 146 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 0.010 0.001 PHE A 554 TYR 0.012 0.001 TYR A 411 ARG 0.002 0.000 ARG A 348 *********************** 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 38 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.555 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1635 time to fit residues: 7.9159 Evaluate side-chains 32 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.0170 chunk 47 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4713 Z= 0.156 Angle : 0.490 5.593 6357 Z= 0.261 Chirality : 0.037 0.149 706 Planarity : 0.003 0.030 828 Dihedral : 3.987 21.067 622 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.17 % Allowed : 16.14 % 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: 1.57 (0.36), residues: 579 helix: 1.82 (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 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 67 PHE 0.010 0.001 PHE A 554 TYR 0.010 0.001 TYR A 161 ARG 0.001 0.000 ARG A 197 *********************** 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 42 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.544 Fit side-chains REVERT: A 548 MET cc_start: 0.7426 (tpp) cc_final: 0.7125 (tpp) outliers start: 11 outliers final: 6 residues processed: 40 average time/residue: 0.1371 time to fit residues: 7.9040 Evaluate side-chains 32 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 52 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4713 Z= 0.172 Angle : 0.510 6.183 6357 Z= 0.273 Chirality : 0.037 0.145 706 Planarity : 0.003 0.031 828 Dihedral : 3.981 20.969 622 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.57 % Allowed : 17.13 % 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 (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: 1.84 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.39 (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 0.010 0.001 PHE A 554 TYR 0.010 0.001 TYR A 161 ARG 0.001 0.000 ARG A 197 *********************** 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 fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7397 (tpp) cc_final: 0.7133 (tpp) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1496 time to fit residues: 7.5630 Evaluate side-chains 34 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 289 CYS 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 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4713 Z= 0.158 Angle : 0.481 5.292 6357 Z= 0.257 Chirality : 0.037 0.143 706 Planarity : 0.003 0.039 828 Dihedral : 3.934 20.489 622 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.17 % Allowed : 17.52 % 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 (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: 1.60 (0.36), residues: 579 helix: 1.87 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.41 (0.50), residues: 148 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 0.010 0.001 PHE A 554 TYR 0.011 0.001 TYR A 161 ARG 0.001 0.000 ARG A 197 *********************** 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 40 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7389 (tpp) cc_final: 0.7183 (tpp) outliers start: 11 outliers final: 9 residues processed: 36 average time/residue: 0.1278 time to fit residues: 6.8604 Evaluate side-chains 35 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 150 TYR 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 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4713 Z= 0.162 Angle : 0.493 5.249 6357 Z= 0.264 Chirality : 0.037 0.143 706 Planarity : 0.004 0.045 828 Dihedral : 3.896 20.360 622 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.97 % Allowed : 17.72 % 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 (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: 1.61 (0.36), residues: 579 helix: 1.88 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 148 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 0.014 0.001 PHE A 554 TYR 0.010 0.001 TYR A 161 ARG 0.001 0.000 ARG A 348 ********************** 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 38 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7404 (tpp) cc_final: 0.7199 (tpp) outliers start: 10 outliers final: 8 residues processed: 34 average time/residue: 0.1381 time to fit residues: 6.9228 Evaluate side-chains 35 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 150 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 CYS 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 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101549 restraints weight = 7447.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104513 restraints weight = 4764.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106504 restraints weight = 3576.533| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 4713 Z= 0.175 Angle : 0.505 5.277 6357 Z= 0.269 Chirality : 0.038 0.145 706 Planarity : 0.004 0.049 828 Dihedral : 3.914 20.851 622 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.77 % Allowed : 18.31 % 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: 1.86 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 148 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 0.012 0.001 PHE A 554 TYR 0.010 0.001 TYR A 161 ARG 0.001 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.40 seconds wall clock time: 26 minutes 4.17 seconds (1564.17 seconds total)