Starting phenix.real_space_refine on Tue Jan 14 00:08:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vaf_43090/01_2025/8vaf_43090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vaf_43090/01_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_43090/01_2025/8vaf_43090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vaf_43090/01_2025/8vaf_43090.map" model { file = "/net/cci-nas-00/data/ceres_data/8vaf_43090/01_2025/8vaf_43090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vaf_43090/01_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-5571/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: 4.15, per 1000 atoms: 0.90 Number of scatterers: 4623 At special positions: 0 Unit cell: (66.7, 90.85, 93.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 882 8.00 N 782 7.00 C 2918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 279 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=1.30 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 550.0 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: 0.46 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: 1.23 Time building geometry restraints manager: 1.18 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.270 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.537 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1377 time to fit residues: 8.8500 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 : 0.555 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102175 restraints weight = 7289.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104673 restraints weight = 5098.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106363 restraints weight = 4006.324| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.520 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 0.1355 time to fit residues: 6.9236 Evaluate side-chains 24 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.127284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099225 restraints weight = 7356.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102037 restraints weight = 4829.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103877 restraints weight = 3677.618| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4713 Z= 0.192 Angle : 0.519 6.025 6357 Z= 0.273 Chirality : 0.038 0.152 706 Planarity : 0.004 0.044 828 Dihedral : 4.185 25.746 622 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.18 % Allowed : 11.42 % Favored : 87.40 % 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: 1.75 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -1.26 (0.50), residues: 146 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 0.009 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 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.531 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.1408 time to fit residues: 7.7137 Evaluate side-chains 29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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: 8.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099777 restraints weight = 7407.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102608 restraints weight = 4840.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104600 restraints weight = 3684.806| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1597 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= 0.178 Angle : 0.500 5.886 6357 Z= 0.264 Chirality : 0.038 0.151 706 Planarity : 0.004 0.052 828 Dihedral : 4.120 22.008 622 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.38 % Allowed : 13.39 % Favored : 85.24 % 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: 1.56 (0.36), residues: 579 helix: 1.79 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.27 (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 0.015 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 38 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.554 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 37 average time/residue: 0.1399 time to fit residues: 7.5384 Evaluate side-chains 30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.127101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099442 restraints weight = 7448.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102311 restraints weight = 4887.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104271 restraints weight = 3713.224| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4713 Z= 0.177 Angle : 0.499 5.698 6357 Z= 0.264 Chirality : 0.038 0.151 706 Planarity : 0.003 0.030 828 Dihedral : 4.058 24.286 622 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.77 % Allowed : 14.17 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.36), residues: 579 helix: 1.82 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.28 (0.51), 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 *********************** 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 36 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.498 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 33 average time/residue: 0.1518 time to fit residues: 7.4685 Evaluate side-chains 31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099357 restraints weight = 7424.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102122 restraints weight = 4938.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104059 restraints weight = 3756.637| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4713 Z= 0.191 Angle : 0.521 6.959 6357 Z= 0.276 Chirality : 0.038 0.152 706 Planarity : 0.003 0.030 828 Dihedral : 3.987 22.648 622 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: 1.72 (0.36), residues: 579 helix: 1.93 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -1.14 (0.51), residues: 153 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 0.011 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 39 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.551 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.1751 time to fit residues: 8.4642 Evaluate side-chains 31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 554 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.125710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098188 restraints weight = 7405.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101000 restraints weight = 4880.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102920 restraints weight = 3710.477| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1997 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= 0.192 Angle : 0.505 5.622 6357 Z= 0.267 Chirality : 0.038 0.153 706 Planarity : 0.003 0.030 828 Dihedral : 4.010 22.196 622 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.97 % Allowed : 15.75 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.36), residues: 579 helix: 1.83 (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 0.009 0.001 PHE A 554 TYR 0.011 0.001 TYR A 411 ARG 0.002 0.000 ARG A 257 *********************** 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 41 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.559 Fit side-chains REVERT: A 548 MET cc_start: 0.7495 (tpp) cc_final: 0.7184 (tpp) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 0.1567 time to fit residues: 8.8791 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 : 0.682 ------------------------------------------------------------------------------- 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 554 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.127026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099765 restraints weight = 7283.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102602 restraints weight = 4864.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104475 restraints weight = 3697.183| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4713 Z= 0.161 Angle : 0.485 5.413 6357 Z= 0.260 Chirality : 0.037 0.147 706 Planarity : 0.003 0.033 828 Dihedral : 3.914 21.094 622 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.77 % Allowed : 16.73 % Favored : 81.50 % 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: 1.64 (0.36), residues: 579 helix: 1.91 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.43 (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 348 *********************** 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 41 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.528 Fit side-chains REVERT: A 548 MET cc_start: 0.7459 (tpp) cc_final: 0.7207 (tpp) outliers start: 9 outliers final: 7 residues processed: 37 average time/residue: 0.1400 time to fit residues: 7.4337 Evaluate side-chains 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.125962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098593 restraints weight = 7460.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101370 restraints weight = 4933.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103316 restraints weight = 3767.450| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4713 Z= 0.188 Angle : 0.507 5.438 6357 Z= 0.271 Chirality : 0.038 0.151 706 Planarity : 0.004 0.041 828 Dihedral : 3.946 21.883 622 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.57 % Allowed : 17.52 % 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: 1.61 (0.36), residues: 579 helix: 1.87 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.40 (0.50), 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 0.012 0.001 PHE A 554 TYR 0.011 0.001 TYR A 411 ARG 0.002 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.519 Fit side-chains REVERT: A 548 MET cc_start: 0.7550 (tpp) cc_final: 0.7257 (tpp) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.1434 time to fit residues: 7.2786 Evaluate side-chains 36 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.0070 chunk 53 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.128026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100901 restraints weight = 7388.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103922 restraints weight = 4683.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105938 restraints weight = 3500.682| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4713 Z= 0.190 Angle : 0.513 5.441 6357 Z= 0.274 Chirality : 0.038 0.150 706 Planarity : 0.004 0.045 828 Dihedral : 4.014 21.796 622 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.57 % Allowed : 17.91 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.50), 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 0.016 0.001 PHE A 102 TYR 0.011 0.001 TYR A 161 ARG 0.002 0.000 ARG A 257 ********************** 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 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.7526 (tpp) cc_final: 0.7252 (tpp) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1364 time to fit residues: 7.2460 Evaluate side-chains 36 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.127364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100242 restraints weight = 7517.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103238 restraints weight = 4743.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105209 restraints weight = 3535.492| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4713 Z= 0.196 Angle : 0.520 5.605 6357 Z= 0.276 Chirality : 0.038 0.153 706 Planarity : 0.004 0.049 828 Dihedral : 4.047 22.319 622 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.57 % Allowed : 18.31 % 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: 1.81 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -1.41 (0.49), 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 0.011 0.001 TYR A 411 ARG 0.002 0.000 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.71 seconds wall clock time: 34 minutes 38.47 seconds (2078.47 seconds total)