Starting phenix.real_space_refine on Sat Apr 26 15:52:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gx5_0077/04_2025/6gx5_0077.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gx5_0077/04_2025/6gx5_0077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gx5_0077/04_2025/6gx5_0077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gx5_0077/04_2025/6gx5_0077.map" model { file = "/net/cci-nas-00/data/ceres_data/6gx5_0077/04_2025/6gx5_0077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gx5_0077/04_2025/6gx5_0077.cif" } resolution = 3.2 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= 0.002 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 3 5.16 5 C 1335 2.51 5 N 396 2.21 5 O 399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2133 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Restraints were copied for chains: C, B Time building chain proxies: 1.88, per 1000 atoms: 0.88 Number of scatterers: 2133 At special positions: 0 Unit cell: (110.4, 81.65, 40.25, 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 3 16.00 O 399 8.00 N 396 7.00 C 1335 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: 0.47 Conformation dependent library (CDL) restraints added in 269.3 milliseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 87.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 255 through 260 removed outlier: 6.408A pdb=" N ASN A 255 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER C 258 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 257 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ILE C 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS A 259 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.637A pdb=" N THR A 263 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN A 265 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS B 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS A 267 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 274 through 310 removed outlier: 6.458A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.035A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.462A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.266A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.123A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 354 removed outlier: 9.047A pdb=" N GLN A 336 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LYS B 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS B 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 346 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ARG B 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP A 348 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN B 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 337 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU C 338 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 339 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS C 340 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER A 341 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU C 342 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.787A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 369 through 377 removed outlier: 6.908A pdb=" N LYS A 370 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 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: 0.50 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 363 1.32 - 1.44: 504 1.44 - 1.56: 1247 1.56 - 1.69: 49 1.69 - 1.81: 3 Bond restraints: 2166 Sorted by residual: bond pdb=" N GLN B 269 " pdb=" CA GLN B 269 " ideal model delta sigma weight residual 1.457 1.533 -0.076 1.41e-02 5.03e+03 2.92e+01 bond pdb=" N GLN A 269 " pdb=" CA GLN A 269 " ideal model delta sigma weight residual 1.457 1.532 -0.076 1.41e-02 5.03e+03 2.87e+01 bond pdb=" N GLN C 269 " pdb=" CA GLN C 269 " ideal model delta sigma weight residual 1.457 1.532 -0.075 1.41e-02 5.03e+03 2.84e+01 bond pdb=" N LEU B 376 " pdb=" CA LEU B 376 " ideal model delta sigma weight residual 1.454 1.519 -0.064 1.27e-02 6.20e+03 2.56e+01 bond pdb=" N LEU A 376 " pdb=" CA LEU A 376 " ideal model delta sigma weight residual 1.454 1.518 -0.064 1.27e-02 6.20e+03 2.52e+01 ... (remaining 2161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 2589 1.73 - 3.46: 243 3.46 - 5.20: 42 5.20 - 6.93: 13 6.93 - 8.66: 5 Bond angle restraints: 2892 Sorted by residual: angle pdb=" N LYS B 340 " pdb=" CA LYS B 340 " pdb=" C LYS B 340 " ideal model delta sigma weight residual 109.24 114.94 -5.70 1.67e+00 3.59e-01 1.17e+01 angle pdb=" N LYS A 340 " pdb=" CA LYS A 340 " pdb=" C LYS A 340 " ideal model delta sigma weight residual 109.24 114.92 -5.68 1.67e+00 3.59e-01 1.15e+01 angle pdb=" N LYS C 340 " pdb=" CA LYS C 340 " pdb=" C LYS C 340 " ideal model delta sigma weight residual 109.24 114.90 -5.66 1.67e+00 3.59e-01 1.15e+01 angle pdb=" N GLU C 338 " pdb=" CA GLU C 338 " pdb=" C GLU C 338 " ideal model delta sigma weight residual 108.76 114.44 -5.68 1.69e+00 3.50e-01 1.13e+01 angle pdb=" N GLU A 338 " pdb=" CA GLU A 338 " pdb=" C GLU A 338 " ideal model delta sigma weight residual 108.76 114.42 -5.66 1.69e+00 3.50e-01 1.12e+01 ... (remaining 2887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.95: 1103 13.95 - 27.90: 139 27.90 - 41.85: 63 41.85 - 55.80: 15 55.80 - 69.76: 6 Dihedral angle restraints: 1326 sinusoidal: 558 harmonic: 768 Sorted by residual: dihedral pdb=" CA ASP C 358 " pdb=" C ASP C 358 " pdb=" N ASN C 359 " pdb=" CA ASN C 359 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP B 358 " pdb=" C ASP B 358 " pdb=" N ASN B 359 " pdb=" CA ASN B 359 " ideal model delta harmonic sigma weight residual 180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP A 358 " pdb=" C ASP A 358 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 1323 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.066: 162 0.066 - 0.132: 90 0.132 - 0.198: 48 0.198 - 0.264: 6 0.264 - 0.330: 15 Chirality restraints: 321 Sorted by residual: chirality pdb=" CA PRO C 270 " pdb=" N PRO C 270 " pdb=" C PRO C 270 " pdb=" CB PRO C 270 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" C PRO B 270 " pdb=" CB PRO B 270 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA PRO A 270 " pdb=" N PRO A 270 " pdb=" C PRO A 270 " pdb=" CB PRO A 270 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 318 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO B 364 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 330 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C HIS B 330 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS B 330 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS B 331 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " -0.039 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 364 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.034 5.00e-02 4.00e+02 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 1078 3.06 - 3.52: 1856 3.52 - 3.98: 3364 3.98 - 4.44: 3156 4.44 - 4.90: 6687 Nonbonded interactions: 16141 Sorted by model distance: nonbonded pdb=" O HIS A 268 " pdb=" N GLN C 269 " model vdw 2.596 3.120 nonbonded pdb=" N GLN A 269 " pdb=" O HIS B 268 " model vdw 2.597 3.120 nonbonded pdb=" OG1 THR B 361 " pdb=" OG1 THR B 373 " model vdw 2.629 3.040 nonbonded pdb=" OG1 THR C 361 " pdb=" OG1 THR C 373 " model vdw 2.629 3.040 nonbonded pdb=" OG1 THR A 361 " pdb=" OG1 THR A 373 " model vdw 2.630 3.040 ... (remaining 16136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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 individual isotropic 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: 0.920 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.017 0.076 2166 Z= 1.190 Angle : 1.199 8.660 2892 Z= 0.690 Chirality : 0.111 0.330 321 Planarity : 0.012 0.061 369 Dihedral : 16.090 69.756 840 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.94 % Allowed : 9.88 % Favored : 85.19 % 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: -3.50 (0.34), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.26), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS C 362 PHE 0.038 0.011 PHE C 346 TYR 0.025 0.009 TYR C 310 ARG 0.002 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.10999 ( 44) hydrogen bonds : angle 7.45897 ( 132) covalent geometry : bond 0.01746 ( 2166) covalent geometry : angle 1.19897 ( 2892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7241 (tptm) cc_final: 0.7026 (tptm) REVERT: A 317 LYS cc_start: 0.8515 (ptmt) cc_final: 0.8304 (ptpp) REVERT: A 347 LYS cc_start: 0.8368 (mttt) cc_final: 0.8072 (mttp) REVERT: A 359 ASN cc_start: 0.8657 (t0) cc_final: 0.8449 (t0) REVERT: A 369 LYS cc_start: 0.8701 (mttt) cc_final: 0.8452 (mttt) REVERT: B 257 LYS cc_start: 0.8521 (mttt) cc_final: 0.8299 (ttmm) REVERT: B 345 ASP cc_start: 0.8573 (t0) cc_final: 0.8320 (t0) REVERT: B 347 LYS cc_start: 0.7988 (mttt) cc_final: 0.7713 (mttp) REVERT: B 353 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8298 (mtpp) REVERT: B 356 SER cc_start: 0.8849 (p) cc_final: 0.8584 (p) REVERT: B 359 ASN cc_start: 0.8627 (t0) cc_final: 0.8198 (t0) outliers start: 12 outliers final: 2 residues processed: 81 average time/residue: 0.3186 time to fit residues: 27.6764 Evaluate side-chains 70 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 357 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059594 restraints weight = 3513.343| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.50 r_work: 0.2751 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2166 Z= 0.192 Angle : 0.605 6.193 2892 Z= 0.299 Chirality : 0.050 0.130 321 Planarity : 0.006 0.045 369 Dihedral : 6.263 44.907 289 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.29 % Allowed : 16.05 % Favored : 80.66 % 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: -3.20 (0.36), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.28), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.014 0.002 PHE A 378 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01989 ( 44) hydrogen bonds : angle 5.49872 ( 132) covalent geometry : bond 0.00481 ( 2166) covalent geometry : angle 0.60454 ( 2892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7319 (tptm) cc_final: 0.7021 (tptm) REVERT: A 267 LYS cc_start: 0.8419 (mttt) cc_final: 0.8207 (mmtt) REVERT: A 310 TYR cc_start: 0.9139 (t80) cc_final: 0.8821 (t80) REVERT: A 317 LYS cc_start: 0.8343 (ptmt) cc_final: 0.7905 (ptpp) REVERT: A 338 GLU cc_start: 0.8428 (pt0) cc_final: 0.8026 (pt0) REVERT: A 345 ASP cc_start: 0.7979 (t0) cc_final: 0.7684 (t0) REVERT: A 347 LYS cc_start: 0.7972 (mttt) cc_final: 0.7647 (mttp) REVERT: A 359 ASN cc_start: 0.9040 (t0) cc_final: 0.8743 (t0) REVERT: B 254 LYS cc_start: 0.7741 (tptm) cc_final: 0.7435 (tptm) REVERT: B 257 LYS cc_start: 0.8337 (mttt) cc_final: 0.8007 (ttmm) REVERT: B 338 GLU cc_start: 0.8568 (pt0) cc_final: 0.7680 (pt0) REVERT: B 340 LYS cc_start: 0.8510 (mttt) cc_final: 0.7962 (mttt) REVERT: B 345 ASP cc_start: 0.8461 (t0) cc_final: 0.8077 (t70) REVERT: B 347 LYS cc_start: 0.7975 (mttt) cc_final: 0.7748 (mttp) REVERT: B 359 ASN cc_start: 0.8775 (t0) cc_final: 0.8368 (t0) REVERT: C 269 GLN cc_start: 0.8857 (mp10) cc_final: 0.8486 (mp10) REVERT: C 370 LYS cc_start: 0.8781 (mttt) cc_final: 0.8499 (mppt) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 0.3160 time to fit residues: 26.4596 Evaluate side-chains 73 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059090 restraints weight = 3495.408| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.49 r_work: 0.2757 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2166 Z= 0.181 Angle : 0.551 5.164 2892 Z= 0.276 Chirality : 0.049 0.130 321 Planarity : 0.005 0.037 369 Dihedral : 5.573 36.372 287 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.47 % Allowed : 18.93 % Favored : 78.60 % 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: -3.06 (0.38), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE A 378 TYR 0.019 0.003 TYR C 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01715 ( 44) hydrogen bonds : angle 5.05327 ( 132) covalent geometry : bond 0.00446 ( 2166) covalent geometry : angle 0.55142 ( 2892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7272 (tptm) cc_final: 0.7032 (tptm) REVERT: A 267 LYS cc_start: 0.8371 (mttt) cc_final: 0.8135 (mmtt) REVERT: A 317 LYS cc_start: 0.8325 (ptmt) cc_final: 0.7908 (ptpp) REVERT: A 338 GLU cc_start: 0.8369 (pt0) cc_final: 0.8022 (pt0) REVERT: A 345 ASP cc_start: 0.7974 (t0) cc_final: 0.7741 (t0) REVERT: A 347 LYS cc_start: 0.7920 (mttt) cc_final: 0.7609 (mttp) REVERT: A 353 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8356 (mtpp) REVERT: A 359 ASN cc_start: 0.8926 (t0) cc_final: 0.8566 (t0) REVERT: B 254 LYS cc_start: 0.7751 (tptm) cc_final: 0.7472 (tptm) REVERT: B 264 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7661 (mp0) REVERT: B 338 GLU cc_start: 0.8603 (pt0) cc_final: 0.8064 (pt0) REVERT: B 340 LYS cc_start: 0.8541 (mttt) cc_final: 0.8233 (mmtt) REVERT: B 359 ASN cc_start: 0.8774 (t0) cc_final: 0.8255 (t0) REVERT: C 370 LYS cc_start: 0.8820 (mttt) cc_final: 0.8501 (mppt) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.3511 time to fit residues: 26.2188 Evaluate side-chains 72 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058772 restraints weight = 3538.129| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.47 r_work: 0.2741 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2166 Z= 0.210 Angle : 0.573 6.605 2892 Z= 0.283 Chirality : 0.050 0.133 321 Planarity : 0.005 0.036 369 Dihedral : 5.592 38.451 287 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.29 % Allowed : 18.52 % Favored : 78.19 % 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: -2.99 (0.39), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.009 0.002 PHE A 378 TYR 0.020 0.003 TYR B 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01687 ( 44) hydrogen bonds : angle 4.82725 ( 132) covalent geometry : bond 0.00514 ( 2166) covalent geometry : angle 0.57306 ( 2892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7281 (tptm) cc_final: 0.7056 (tptm) REVERT: A 267 LYS cc_start: 0.8393 (mttt) cc_final: 0.8147 (mmtt) REVERT: A 310 TYR cc_start: 0.9203 (t80) cc_final: 0.8907 (t80) REVERT: A 317 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7989 (ptpp) REVERT: A 338 GLU cc_start: 0.8357 (pt0) cc_final: 0.8021 (pt0) REVERT: A 345 ASP cc_start: 0.8057 (t0) cc_final: 0.7850 (t0) REVERT: A 347 LYS cc_start: 0.7974 (mttt) cc_final: 0.7644 (mttp) REVERT: A 353 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8326 (mtpp) REVERT: A 359 ASN cc_start: 0.8949 (t0) cc_final: 0.8650 (t0) REVERT: B 254 LYS cc_start: 0.7744 (tptm) cc_final: 0.7467 (tptm) REVERT: B 264 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7720 (mp0) REVERT: B 338 GLU cc_start: 0.8609 (pt0) cc_final: 0.8089 (pt0) REVERT: B 340 LYS cc_start: 0.8515 (mttt) cc_final: 0.8222 (mmtt) REVERT: B 359 ASN cc_start: 0.8772 (t0) cc_final: 0.8229 (t0) REVERT: B 370 LYS cc_start: 0.8691 (mttt) cc_final: 0.8384 (mttt) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.3518 time to fit residues: 27.4151 Evaluate side-chains 73 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058523 restraints weight = 3601.023| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.51 r_work: 0.2752 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2166 Z= 0.202 Angle : 0.569 7.505 2892 Z= 0.279 Chirality : 0.050 0.130 321 Planarity : 0.004 0.035 369 Dihedral : 5.542 41.525 287 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.53 % Allowed : 16.87 % Favored : 78.60 % 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: -2.96 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.008 0.001 PHE A 378 TYR 0.021 0.004 TYR C 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01567 ( 44) hydrogen bonds : angle 4.65674 ( 132) covalent geometry : bond 0.00490 ( 2166) covalent geometry : angle 0.56878 ( 2892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7327 (tptm) cc_final: 0.7098 (tptm) REVERT: A 267 LYS cc_start: 0.8415 (mttt) cc_final: 0.8154 (mmtt) REVERT: A 317 LYS cc_start: 0.8338 (ptmt) cc_final: 0.7949 (ptpp) REVERT: A 338 GLU cc_start: 0.8353 (pt0) cc_final: 0.8042 (pt0) REVERT: A 345 ASP cc_start: 0.8019 (t0) cc_final: 0.7810 (t0) REVERT: A 347 LYS cc_start: 0.7964 (mttt) cc_final: 0.7649 (mttp) REVERT: A 353 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8356 (mtpp) REVERT: A 359 ASN cc_start: 0.8930 (t0) cc_final: 0.8611 (t0) REVERT: A 375 LYS cc_start: 0.8565 (tptt) cc_final: 0.8358 (tttm) REVERT: B 254 LYS cc_start: 0.7751 (tptm) cc_final: 0.7490 (tptm) REVERT: B 264 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7758 (mp0) REVERT: B 338 GLU cc_start: 0.8560 (pt0) cc_final: 0.8070 (pt0) REVERT: B 340 LYS cc_start: 0.8535 (mttt) cc_final: 0.8304 (mmtt) REVERT: B 359 ASN cc_start: 0.8753 (t0) cc_final: 0.8182 (t0) REVERT: B 370 LYS cc_start: 0.8715 (mttt) cc_final: 0.8425 (mttt) REVERT: C 317 LYS cc_start: 0.8427 (ptmt) cc_final: 0.8126 (ptpp) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.3340 time to fit residues: 28.3330 Evaluate side-chains 78 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.068373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058640 restraints weight = 3603.901| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.51 r_work: 0.2751 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2166 Z= 0.187 Angle : 0.583 6.774 2892 Z= 0.280 Chirality : 0.050 0.128 321 Planarity : 0.004 0.033 369 Dihedral : 5.467 43.335 287 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.88 % Allowed : 20.16 % Favored : 76.95 % 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: -2.90 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.007 0.001 PHE A 378 TYR 0.022 0.004 TYR B 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01463 ( 44) hydrogen bonds : angle 4.52942 ( 132) covalent geometry : bond 0.00454 ( 2166) covalent geometry : angle 0.58309 ( 2892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7283 (tptm) cc_final: 0.7069 (tptm) REVERT: A 267 LYS cc_start: 0.8384 (mttt) cc_final: 0.8136 (mmtt) REVERT: A 317 LYS cc_start: 0.8332 (ptmt) cc_final: 0.7933 (ptpp) REVERT: A 338 GLU cc_start: 0.8340 (pt0) cc_final: 0.8023 (pt0) REVERT: A 345 ASP cc_start: 0.8006 (t0) cc_final: 0.7799 (t0) REVERT: A 347 LYS cc_start: 0.7940 (mttt) cc_final: 0.7660 (mttp) REVERT: A 353 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8333 (mtpp) REVERT: A 359 ASN cc_start: 0.8926 (t0) cc_final: 0.8686 (t0) REVERT: B 254 LYS cc_start: 0.7761 (tptm) cc_final: 0.7458 (tptm) REVERT: B 264 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7750 (mp0) REVERT: B 338 GLU cc_start: 0.8555 (pt0) cc_final: 0.8064 (pt0) REVERT: B 340 LYS cc_start: 0.8559 (mttt) cc_final: 0.8301 (mmtt) REVERT: B 359 ASN cc_start: 0.8748 (t0) cc_final: 0.8293 (t0) REVERT: B 370 LYS cc_start: 0.8719 (mttt) cc_final: 0.8415 (mttt) REVERT: C 317 LYS cc_start: 0.8430 (ptmt) cc_final: 0.8113 (ptpp) REVERT: C 370 LYS cc_start: 0.8854 (mttt) cc_final: 0.8521 (mppt) outliers start: 7 outliers final: 7 residues processed: 71 average time/residue: 0.3504 time to fit residues: 26.5659 Evaluate side-chains 75 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 5 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 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057738 restraints weight = 3665.627| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.51 r_work: 0.2731 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2166 Z= 0.232 Angle : 0.614 6.950 2892 Z= 0.296 Chirality : 0.050 0.135 321 Planarity : 0.004 0.033 369 Dihedral : 5.629 46.066 287 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.70 % Allowed : 20.58 % Favored : 75.72 % 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: -2.89 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.009 0.002 PHE A 378 TYR 0.023 0.004 TYR B 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01544 ( 44) hydrogen bonds : angle 4.57589 ( 132) covalent geometry : bond 0.00563 ( 2166) covalent geometry : angle 0.61445 ( 2892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7357 (tptm) cc_final: 0.7131 (tptm) REVERT: A 267 LYS cc_start: 0.8386 (mttt) cc_final: 0.8125 (mmtt) REVERT: A 317 LYS cc_start: 0.8322 (ptmt) cc_final: 0.7931 (ptpp) REVERT: A 338 GLU cc_start: 0.8374 (pt0) cc_final: 0.8008 (pt0) REVERT: A 347 LYS cc_start: 0.7956 (mttt) cc_final: 0.7668 (mttp) REVERT: A 359 ASN cc_start: 0.8923 (t0) cc_final: 0.8624 (t0) REVERT: B 254 LYS cc_start: 0.7837 (tptm) cc_final: 0.7562 (tptm) REVERT: B 264 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7742 (mp0) REVERT: B 338 GLU cc_start: 0.8548 (pt0) cc_final: 0.8064 (pt0) REVERT: B 359 ASN cc_start: 0.8740 (t0) cc_final: 0.8249 (t0) REVERT: B 370 LYS cc_start: 0.8714 (mttt) cc_final: 0.8397 (mttt) REVERT: C 317 LYS cc_start: 0.8430 (ptmt) cc_final: 0.8202 (ptpp) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.3431 time to fit residues: 26.1034 Evaluate side-chains 74 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 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 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057664 restraints weight = 3693.925| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.56 r_work: 0.2787 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2166 Z= 0.213 Angle : 0.630 6.558 2892 Z= 0.299 Chirality : 0.050 0.125 321 Planarity : 0.004 0.032 369 Dihedral : 5.572 46.903 287 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.12 % Allowed : 20.99 % Favored : 74.90 % 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: -2.89 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.008 0.001 PHE A 378 TYR 0.023 0.004 TYR B 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01559 ( 44) hydrogen bonds : angle 4.56073 ( 132) covalent geometry : bond 0.00516 ( 2166) covalent geometry : angle 0.62953 ( 2892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7359 (tptm) cc_final: 0.7147 (tptm) REVERT: A 267 LYS cc_start: 0.8412 (mttt) cc_final: 0.8143 (mmtt) REVERT: A 317 LYS cc_start: 0.8334 (ptmt) cc_final: 0.7982 (ptpp) REVERT: A 338 GLU cc_start: 0.8376 (pt0) cc_final: 0.8016 (pt0) REVERT: A 347 LYS cc_start: 0.7951 (mttt) cc_final: 0.7666 (mttp) REVERT: A 359 ASN cc_start: 0.8931 (t0) cc_final: 0.8646 (t0) REVERT: B 254 LYS cc_start: 0.7891 (tptm) cc_final: 0.7589 (tptm) REVERT: B 264 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7760 (mp0) REVERT: B 307 GLN cc_start: 0.8672 (mt0) cc_final: 0.8425 (mt0) REVERT: B 338 GLU cc_start: 0.8557 (pt0) cc_final: 0.8054 (pt0) REVERT: B 359 ASN cc_start: 0.8744 (t0) cc_final: 0.8265 (t0) REVERT: B 370 LYS cc_start: 0.8761 (mttt) cc_final: 0.8456 (mttt) REVERT: C 317 LYS cc_start: 0.8446 (ptmt) cc_final: 0.8209 (ptpp) outliers start: 10 outliers final: 9 residues processed: 72 average time/residue: 0.3321 time to fit residues: 25.5330 Evaluate side-chains 77 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058472 restraints weight = 3663.860| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.55 r_work: 0.2762 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2166 Z= 0.180 Angle : 0.613 7.104 2892 Z= 0.289 Chirality : 0.050 0.119 321 Planarity : 0.004 0.030 369 Dihedral : 5.444 46.939 287 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.53 % Allowed : 20.99 % Favored : 74.49 % 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: -2.86 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.025 0.004 TYR B 310 ARG 0.000 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01398 ( 44) hydrogen bonds : angle 4.50228 ( 132) covalent geometry : bond 0.00435 ( 2166) covalent geometry : angle 0.61283 ( 2892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: A 267 LYS cc_start: 0.8392 (mttt) cc_final: 0.8116 (mmtt) REVERT: A 317 LYS cc_start: 0.8367 (ptmt) cc_final: 0.8018 (ptpp) REVERT: A 338 GLU cc_start: 0.8354 (pt0) cc_final: 0.8001 (pt0) REVERT: A 347 LYS cc_start: 0.7913 (mttt) cc_final: 0.7652 (mttp) REVERT: A 359 ASN cc_start: 0.8902 (t0) cc_final: 0.8637 (t0) REVERT: B 254 LYS cc_start: 0.7779 (tptm) cc_final: 0.7507 (tptm) REVERT: B 264 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7799 (mp0) REVERT: B 307 GLN cc_start: 0.8663 (mt0) cc_final: 0.8411 (mt0) REVERT: B 338 GLU cc_start: 0.8505 (pt0) cc_final: 0.7996 (pt0) REVERT: B 359 ASN cc_start: 0.8742 (t0) cc_final: 0.8257 (t0) REVERT: B 369 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8748 (mtpp) REVERT: C 317 LYS cc_start: 0.8444 (ptmt) cc_final: 0.8211 (ptpp) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.3137 time to fit residues: 25.5801 Evaluate side-chains 78 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 11 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059137 restraints weight = 3609.778| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.51 r_work: 0.2825 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2166 Z= 0.153 Angle : 0.627 8.401 2892 Z= 0.291 Chirality : 0.050 0.119 321 Planarity : 0.004 0.031 369 Dihedral : 5.329 46.644 287 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.70 % Allowed : 22.63 % Favored : 73.66 % 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: -2.86 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.006 0.001 PHE B 346 TYR 0.024 0.004 TYR B 310 ARG 0.000 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01245 ( 44) hydrogen bonds : angle 4.32344 ( 132) covalent geometry : bond 0.00372 ( 2166) covalent geometry : angle 0.62748 ( 2892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: A 267 LYS cc_start: 0.8413 (mttt) cc_final: 0.8143 (mmtt) REVERT: A 317 LYS cc_start: 0.8393 (ptmt) cc_final: 0.8053 (ptpp) REVERT: A 338 GLU cc_start: 0.8365 (pt0) cc_final: 0.8024 (pt0) REVERT: A 347 LYS cc_start: 0.7896 (mttt) cc_final: 0.7622 (mttp) REVERT: A 359 ASN cc_start: 0.8905 (t0) cc_final: 0.8660 (t0) REVERT: B 254 LYS cc_start: 0.7782 (tptm) cc_final: 0.7575 (tptm) REVERT: B 264 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7770 (mp0) REVERT: B 307 GLN cc_start: 0.8695 (mt0) cc_final: 0.8442 (mt0) REVERT: B 338 GLU cc_start: 0.8507 (pt0) cc_final: 0.7985 (pt0) REVERT: B 359 ASN cc_start: 0.8742 (t0) cc_final: 0.8287 (t0) REVERT: B 372 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: C 269 GLN cc_start: 0.8806 (mp10) cc_final: 0.8593 (mp10) REVERT: C 317 LYS cc_start: 0.8437 (ptmt) cc_final: 0.8205 (ptpp) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.3425 time to fit residues: 27.0646 Evaluate side-chains 78 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 22 optimal weight: 0.0470 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059195 restraints weight = 3587.991| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.52 r_work: 0.2821 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2166 Z= 0.165 Angle : 0.647 10.160 2892 Z= 0.297 Chirality : 0.050 0.119 321 Planarity : 0.004 0.030 369 Dihedral : 5.317 46.626 287 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.53 % Allowed : 20.99 % Favored : 74.49 % 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: -2.83 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.024 0.004 TYR B 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01219 ( 44) hydrogen bonds : angle 4.27632 ( 132) covalent geometry : bond 0.00403 ( 2166) covalent geometry : angle 0.64680 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1937.37 seconds wall clock time: 34 minutes 5.16 seconds (2045.16 seconds total)