Starting phenix.real_space_refine on Wed Mar 5 18:50:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x12_21986/03_2025/6x12_21986.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x12_21986/03_2025/6x12_21986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x12_21986/03_2025/6x12_21986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x12_21986/03_2025/6x12_21986.map" model { file = "/net/cci-nas-00/data/ceres_data/6x12_21986/03_2025/6x12_21986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x12_21986/03_2025/6x12_21986.cif" } resolution = 3.52 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= 0.003 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 2019 2.51 5 N 486 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3059 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3017 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 17, 'TRANS': 389} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.59, per 1000 atoms: 0.85 Number of scatterers: 3059 At special positions: 0 Unit cell: (67.6148, 79.4205, 69.7613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 535 8.00 N 486 7.00 C 2019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.68 Conformation dependent library (CDL) restraints added in 380.9 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 12 through 32 removed outlier: 3.791A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.518A pdb=" N THR A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.535A pdb=" N LEU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.784A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 3.557A pdb=" N LEU A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.635A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 170 removed outlier: 3.526A pdb=" N ILE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 220 removed outlier: 3.631A pdb=" N VAL A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 254 removed outlier: 3.827A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.617A pdb=" N PHE A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.523A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.725A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 removed outlier: 4.277A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 349 removed outlier: 4.078A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.708A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 382 through 389 removed outlier: 3.850A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 417 removed outlier: 4.021A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 469 1.31 - 1.43: 763 1.43 - 1.56: 1835 1.56 - 1.68: 14 1.68 - 1.81: 34 Bond restraints: 3115 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.409 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C39 6OU A 501 " pdb=" C40 6OU A 501 " ideal model delta sigma weight residual 1.497 1.569 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C15 6OU A 501 " pdb=" C16 6OU A 501 " ideal model delta sigma weight residual 1.501 1.563 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C38 6OU A 501 " pdb=" C39 6OU A 501 " ideal model delta sigma weight residual 1.530 1.582 -0.052 2.00e-02 2.50e+03 6.85e+00 ... (remaining 3110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 4145 2.96 - 5.93: 75 5.93 - 8.89: 11 8.89 - 11.86: 5 11.86 - 14.82: 1 Bond angle restraints: 4237 Sorted by residual: angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 108.77 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N THR A 375 " pdb=" CA THR A 375 " pdb=" C THR A 375 " ideal model delta sigma weight residual 114.04 108.42 5.62 1.24e+00 6.50e-01 2.05e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 119.02 -9.21 2.21e+00 2.05e-01 1.74e+01 angle pdb=" C THR A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 122.95 118.55 4.40 1.24e+00 6.50e-01 1.26e+01 angle pdb=" C THR A 281 " pdb=" N LEU A 282 " pdb=" CA LEU A 282 " ideal model delta sigma weight residual 120.09 124.47 -4.38 1.25e+00 6.40e-01 1.23e+01 ... (remaining 4232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.79: 1748 27.79 - 55.58: 82 55.58 - 83.38: 10 83.38 - 111.17: 3 111.17 - 138.96: 1 Dihedral angle restraints: 1844 sinusoidal: 689 harmonic: 1155 Sorted by residual: dihedral pdb=" C43 6OU A 501 " pdb=" C44 6OU A 501 " pdb=" C45 6OU A 501 " pdb=" C46 6OU A 501 " ideal model delta sinusoidal sigma weight residual -178.62 -39.66 -138.96 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C19 6OU A 501 " pdb=" C20 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O22 6OU A 501 " ideal model delta sinusoidal sigma weight residual -59.00 35.22 -94.22 1 3.00e+01 1.11e-03 1.15e+01 dihedral pdb=" CA THR A 154 " pdb=" C THR A 154 " pdb=" N ILE A 155 " pdb=" CA ILE A 155 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 1841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 413 0.061 - 0.121: 96 0.121 - 0.182: 17 0.182 - 0.242: 2 0.242 - 0.302: 2 Chirality restraints: 530 Sorted by residual: chirality pdb=" CB ILE A 113 " pdb=" CA ILE A 113 " pdb=" CG1 ILE A 113 " pdb=" CG2 ILE A 113 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A 309 " pdb=" CA ILE A 309 " pdb=" CG1 ILE A 309 " pdb=" CG2 ILE A 309 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 527 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 355 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 356 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 153 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 206 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.034 5.00e-02 4.00e+02 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 966 2.84 - 3.35: 2885 3.35 - 3.87: 4958 3.87 - 4.38: 5530 4.38 - 4.90: 9590 Nonbonded interactions: 23929 Sorted by model distance: nonbonded pdb=" O SER A 349 " pdb=" OG SER A 349 " model vdw 2.322 3.040 nonbonded pdb=" OH TYR A 236 " pdb=" O ILE A 392 " model vdw 2.387 3.040 nonbonded pdb=" NZ LYS A 84 " pdb=" OE2 GLU A 416 " model vdw 2.398 3.120 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.423 3.040 nonbonded pdb=" OD2 ASP A 267 " pdb=" NH2 ARG A 287 " model vdw 2.424 3.120 ... (remaining 23924 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: 0.760 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.008 0.088 3115 Z= 0.523 Angle : 1.079 14.824 4237 Z= 0.580 Chirality : 0.056 0.302 530 Planarity : 0.008 0.063 516 Dihedral : 16.636 138.961 1112 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.29 (0.27), residues: 403 helix: -3.21 (0.17), residues: 348 sheet: None (None), residues: 0 loop : -3.27 (0.66), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 223 PHE 0.010 0.002 PHE A 210 TYR 0.026 0.002 TYR A 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.322 Fit side-chains REVERT: A 5 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7616 (mtt-85) REVERT: A 37 HIS cc_start: 0.7841 (t70) cc_final: 0.7585 (p90) REVERT: A 136 ASP cc_start: 0.8232 (m-30) cc_final: 0.7670 (m-30) REVERT: A 316 LEU cc_start: 0.9196 (mt) cc_final: 0.8985 (mm) REVERT: A 347 LEU cc_start: 0.9059 (tp) cc_final: 0.8818 (tt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1618 time to fit residues: 11.8136 Evaluate side-chains 51 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 chunk 11 optimal weight: 0.0570 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 203 GLN A 338 GLN A 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093895 restraints weight = 4404.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096991 restraints weight = 2270.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098909 restraints weight = 1524.164| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3115 Z= 0.153 Angle : 0.544 6.390 4237 Z= 0.279 Chirality : 0.039 0.114 530 Planarity : 0.005 0.041 516 Dihedral : 10.328 81.302 470 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.47 % Allowed : 12.30 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.52 (0.37), residues: 403 helix: -1.36 (0.25), residues: 350 sheet: None (None), residues: 0 loop : -2.30 (0.78), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 40 PHE 0.004 0.001 PHE A 157 TYR 0.019 0.001 TYR A 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.292 Fit side-chains REVERT: A 5 ARG cc_start: 0.7632 (mtt90) cc_final: 0.7381 (mtp-110) REVERT: A 136 ASP cc_start: 0.8259 (m-30) cc_final: 0.7732 (m-30) REVERT: A 251 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6999 (mm) REVERT: A 269 MET cc_start: 0.8211 (ttm) cc_final: 0.7749 (ttp) REVERT: A 275 THR cc_start: 0.8931 (t) cc_final: 0.8656 (t) REVERT: A 347 LEU cc_start: 0.8948 (tp) cc_final: 0.8740 (tt) REVERT: A 383 TYR cc_start: 0.8819 (t80) cc_final: 0.8608 (t80) outliers start: 11 outliers final: 5 residues processed: 69 average time/residue: 0.1429 time to fit residues: 12.0538 Evaluate side-chains 55 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 259 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.0170 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093003 restraints weight = 4358.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095902 restraints weight = 2251.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097953 restraints weight = 1528.218| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3115 Z= 0.198 Angle : 0.569 6.121 4237 Z= 0.287 Chirality : 0.040 0.141 530 Planarity : 0.004 0.033 516 Dihedral : 9.340 87.457 470 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.42 % Allowed : 14.51 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.41), residues: 403 helix: -0.43 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -2.11 (0.84), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 37 PHE 0.007 0.001 PHE A 324 TYR 0.024 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.256 Fit side-chains REVERT: A 136 ASP cc_start: 0.8209 (m-30) cc_final: 0.7705 (m-30) REVERT: A 251 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7075 (mm) REVERT: A 269 MET cc_start: 0.8283 (ttm) cc_final: 0.7780 (ttp) outliers start: 14 outliers final: 9 residues processed: 59 average time/residue: 0.1094 time to fit residues: 8.3660 Evaluate side-chains 50 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0980 chunk 22 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 14 optimal weight: 0.3980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.094385 restraints weight = 4447.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.097431 restraints weight = 2261.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099610 restraints weight = 1519.438| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3115 Z= 0.152 Angle : 0.550 6.659 4237 Z= 0.269 Chirality : 0.039 0.124 530 Planarity : 0.004 0.031 516 Dihedral : 8.687 82.404 470 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.10 % Allowed : 16.40 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.42), residues: 403 helix: 0.09 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.77 (0.88), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 223 PHE 0.004 0.001 PHE A 261 TYR 0.021 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.298 Fit side-chains REVERT: A 136 ASP cc_start: 0.8218 (m-30) cc_final: 0.7669 (m-30) REVERT: A 220 GLN cc_start: 0.8239 (mm-40) cc_final: 0.8032 (mm-40) REVERT: A 269 MET cc_start: 0.8242 (ttm) cc_final: 0.7730 (ttp) outliers start: 13 outliers final: 10 residues processed: 58 average time/residue: 0.1178 time to fit residues: 8.8743 Evaluate side-chains 53 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 15 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.093270 restraints weight = 4452.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.096382 restraints weight = 2293.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.098477 restraints weight = 1543.604| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3115 Z= 0.194 Angle : 0.570 6.838 4237 Z= 0.278 Chirality : 0.040 0.122 530 Planarity : 0.004 0.031 516 Dihedral : 8.563 81.604 470 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.68 % Allowed : 16.09 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.43), residues: 403 helix: 0.35 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.58 (0.89), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 223 PHE 0.006 0.001 PHE A 324 TYR 0.021 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.321 Fit side-chains REVERT: A 136 ASP cc_start: 0.8244 (m-30) cc_final: 0.7705 (m-30) REVERT: A 251 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7203 (mm) REVERT: A 269 MET cc_start: 0.8286 (ttm) cc_final: 0.7757 (ttp) outliers start: 18 outliers final: 14 residues processed: 64 average time/residue: 0.1086 time to fit residues: 9.1896 Evaluate side-chains 60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090663 restraints weight = 4583.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.093800 restraints weight = 2304.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095815 restraints weight = 1529.736| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3115 Z= 0.188 Angle : 0.571 7.114 4237 Z= 0.277 Chirality : 0.040 0.142 530 Planarity : 0.004 0.030 516 Dihedral : 8.266 79.436 470 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.05 % Allowed : 17.98 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.43), residues: 403 helix: 0.51 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.40 (0.90), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 223 PHE 0.005 0.001 PHE A 273 TYR 0.021 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.296 Fit side-chains REVERT: A 136 ASP cc_start: 0.8219 (m-30) cc_final: 0.7678 (m-30) REVERT: A 220 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7535 (mt0) REVERT: A 251 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7121 (mm) REVERT: A 269 MET cc_start: 0.8281 (ttm) cc_final: 0.7758 (ttp) outliers start: 16 outliers final: 13 residues processed: 62 average time/residue: 0.1131 time to fit residues: 9.2845 Evaluate side-chains 59 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.0070 chunk 27 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.093269 restraints weight = 4446.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096427 restraints weight = 2270.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098524 restraints weight = 1531.390| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3115 Z= 0.160 Angle : 0.559 7.315 4237 Z= 0.270 Chirality : 0.040 0.129 530 Planarity : 0.004 0.057 516 Dihedral : 7.946 76.075 470 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.36 % Allowed : 17.98 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.43), residues: 403 helix: 0.66 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -1.10 (0.92), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 223 PHE 0.005 0.001 PHE A 273 TYR 0.020 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.386 Fit side-chains REVERT: A 220 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7522 (mt0) REVERT: A 251 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7083 (mm) REVERT: A 269 MET cc_start: 0.8273 (ttm) cc_final: 0.7740 (ttp) REVERT: A 365 MET cc_start: 0.8096 (mmm) cc_final: 0.7629 (mmm) REVERT: A 383 TYR cc_start: 0.8876 (t80) cc_final: 0.8665 (t80) outliers start: 17 outliers final: 13 residues processed: 66 average time/residue: 0.1585 time to fit residues: 13.1478 Evaluate side-chains 61 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 316 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 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 203 GLN A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.089924 restraints weight = 4470.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.092981 restraints weight = 2271.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.094866 restraints weight = 1523.617| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3115 Z= 0.229 Angle : 0.604 7.882 4237 Z= 0.291 Chirality : 0.041 0.131 530 Planarity : 0.004 0.037 516 Dihedral : 8.152 79.117 470 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.36 % Allowed : 16.72 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.44), residues: 403 helix: 0.66 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.02 (0.90), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 368 PHE 0.006 0.001 PHE A 324 TYR 0.022 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.305 Fit side-chains REVERT: A 136 ASP cc_start: 0.8069 (m-30) cc_final: 0.7630 (m-30) REVERT: A 251 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7242 (mm) REVERT: A 269 MET cc_start: 0.8396 (ttm) cc_final: 0.7902 (ttp) REVERT: A 335 VAL cc_start: 0.8999 (m) cc_final: 0.8643 (t) outliers start: 17 outliers final: 14 residues processed: 63 average time/residue: 0.1073 time to fit residues: 8.9447 Evaluate side-chains 60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.2980 chunk 13 optimal weight: 0.0040 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 327 ASN A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.092481 restraints weight = 4436.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.095609 restraints weight = 2247.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097659 restraints weight = 1506.007| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3115 Z= 0.170 Angle : 0.591 8.053 4237 Z= 0.282 Chirality : 0.040 0.129 530 Planarity : 0.004 0.030 516 Dihedral : 7.926 75.691 470 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.99 % Allowed : 16.72 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.44), residues: 403 helix: 0.73 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -0.93 (0.93), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.006 0.001 PHE A 273 TYR 0.021 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.326 Fit side-chains REVERT: A 136 ASP cc_start: 0.7966 (m-30) cc_final: 0.7509 (m-30) REVERT: A 220 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7488 (mt0) REVERT: A 251 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7131 (mm) REVERT: A 269 MET cc_start: 0.8368 (ttm) cc_final: 0.7886 (ttp) REVERT: A 335 VAL cc_start: 0.8982 (m) cc_final: 0.8586 (t) REVERT: A 338 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7948 (pt0) outliers start: 19 outliers final: 14 residues processed: 67 average time/residue: 0.1095 time to fit residues: 9.6522 Evaluate side-chains 64 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 318 GLN A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.090458 restraints weight = 4407.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.093568 restraints weight = 2272.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095453 restraints weight = 1539.754| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3115 Z= 0.224 Angle : 0.636 11.235 4237 Z= 0.303 Chirality : 0.041 0.132 530 Planarity : 0.004 0.030 516 Dihedral : 8.016 76.769 470 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.36 % Allowed : 18.30 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.44), residues: 403 helix: 0.74 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.01 (0.91), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 223 PHE 0.006 0.001 PHE A 273 TYR 0.022 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.320 Fit side-chains REVERT: A 136 ASP cc_start: 0.7934 (m-30) cc_final: 0.7504 (m-30) REVERT: A 220 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7508 (mt0) REVERT: A 251 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7223 (mm) REVERT: A 269 MET cc_start: 0.8314 (ttm) cc_final: 0.7797 (ttp) REVERT: A 335 VAL cc_start: 0.8964 (m) cc_final: 0.8595 (t) outliers start: 17 outliers final: 12 residues processed: 62 average time/residue: 0.1273 time to fit residues: 10.2966 Evaluate side-chains 59 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 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 318 GLN A 338 GLN A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.090073 restraints weight = 4505.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.093195 restraints weight = 2291.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.095060 restraints weight = 1542.094| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3115 Z= 0.236 Angle : 0.643 10.680 4237 Z= 0.307 Chirality : 0.041 0.134 530 Planarity : 0.004 0.030 516 Dihedral : 8.096 77.133 470 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.05 % Allowed : 17.98 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.43), residues: 403 helix: 0.71 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -1.02 (0.92), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 223 PHE 0.007 0.001 PHE A 273 TYR 0.022 0.001 TYR A 299 ARG 0.004 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1292.61 seconds wall clock time: 23 minutes 14.33 seconds (1394.33 seconds total)