Starting phenix.real_space_refine on Fri Aug 22 13:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkk_14045/08_2025/7qkk_14045.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkk_14045/08_2025/7qkk_14045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qkk_14045/08_2025/7qkk_14045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkk_14045/08_2025/7qkk_14045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qkk_14045/08_2025/7qkk_14045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkk_14045/08_2025/7qkk_14045.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 S 3 5.16 5 C 1086 2.51 5 N 321 2.21 5 O 324 1.98 5 H 1803 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3537 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.12, per 1000 atoms: 0.32 Number of scatterers: 3537 At special positions: 0 Unit cell: (85.696, 72.512, 37.08, 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 3 16.00 O 324 8.00 N 321 7.00 C 1086 6.00 H 1803 1.00 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: 0.31 Conformation dependent library (CDL) restraints added in 87.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.569A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 307 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR A 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 309 " --> pdb=" O TYR A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.963A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.238A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER A 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B 319 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N CYS A 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS B 321 " --> pdb=" O CYS A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.706A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN B 327 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS B 329 " --> pdb=" O HIS A 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.598A pdb=" N GLN B 336 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B 338 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.472A pdb=" N LYS B 343 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE A 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP B 345 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 351 through 353 removed outlier: 6.635A pdb=" N SER B 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 356 through 361 removed outlier: 6.758A pdb=" N SER B 356 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN A 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 358 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR A 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 360 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 375 16 hydrogen bonds defined for protein. 48 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: 0.80 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1800 1.12 - 1.29: 289 1.29 - 1.46: 513 1.46 - 1.64: 959 1.64 - 1.81: 3 Bond restraints: 3564 Sorted by residual: bond pdb=" ND2 ASN B 368 " pdb="HD21 ASN B 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN A 368 " pdb="HD21 ASN A 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS A 375 " pdb=" H LYS A 375 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN B 368 " pdb="HD22 ASN B 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS A 369 " pdb=" H LYS A 369 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 5229 2.44 - 4.87: 934 4.87 - 7.31: 289 7.31 - 9.75: 33 9.75 - 12.18: 7 Bond angle restraints: 6492 Sorted by residual: angle pdb=" CA HIS C 374 " pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 113.80 123.66 -9.86 1.00e+00 1.00e+00 9.73e+01 angle pdb=" CA HIS A 374 " pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 113.80 122.99 -9.19 1.00e+00 1.00e+00 8.45e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 120.20 11.00 1.30e+00 5.92e-01 7.16e+01 angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 121.33 9.87 1.30e+00 5.92e-01 5.76e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.44e+01 ... (remaining 6487 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.05: 1377 14.05 - 28.10: 136 28.10 - 42.15: 54 42.15 - 56.20: 34 56.20 - 70.25: 40 Dihedral angle restraints: 1641 sinusoidal: 939 harmonic: 702 Sorted by residual: dihedral pdb=" CA LYS B 375 " pdb=" C LYS B 375 " pdb=" N LEU B 376 " pdb=" CA LEU B 376 " ideal model delta harmonic sigma weight residual 180.00 149.29 30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -136.61 14.61 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA LYS C 375 " pdb=" C LYS C 375 " pdb=" N LEU C 376 " pdb=" CA LEU C 376 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 1638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 155 0.091 - 0.182: 80 0.182 - 0.274: 20 0.274 - 0.365: 7 0.365 - 0.456: 2 Chirality restraints: 264 Sorted by residual: chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 261 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " -0.321 2.00e-02 2.50e+03 1.68e-01 6.35e+02 pdb=" CG HIS A 374 " 0.219 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " 0.162 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " 0.167 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 HIS A 374 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 HIS A 374 " -0.147 2.00e-02 2.50e+03 pdb=" HE2 HIS A 374 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " -0.249 2.00e-02 2.50e+03 1.30e-01 3.83e+02 pdb=" CG HIS C 374 " 0.181 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " 0.124 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " 0.129 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " -0.113 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 374 " 0.151 2.00e-02 2.50e+03 8.51e-02 1.63e+02 pdb=" CG HIS B 374 " -0.120 2.00e-02 2.50e+03 pdb=" ND1 HIS B 374 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 HIS B 374 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS B 374 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS B 374 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 HIS B 374 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS B 374 " 0.094 2.00e-02 2.50e+03 pdb=" HE2 HIS B 374 " 0.066 2.00e-02 2.50e+03 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 185 2.14 - 2.76: 5632 2.76 - 3.37: 9537 3.37 - 3.99: 12229 3.99 - 4.60: 17889 Nonbonded interactions: 45472 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.525 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.642 2.450 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ1 LYS B 370 " model vdw 1.674 2.450 nonbonded pdb=" OD2 ASP A 314 " pdb=" HZ2 LYS A 370 " model vdw 1.693 2.450 ... (remaining 45467 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 6.190 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: 0.030 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.012 0.086 1761 Z= 0.753 Angle : 2.170 11.001 2355 Z= 1.448 Chirality : 0.118 0.456 264 Planarity : 0.017 0.155 300 Dihedral : 13.175 70.250 675 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Cbeta Deviations : 2.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.40), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.30), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 379 TYR 0.113 0.039 TYR A 310 PHE 0.021 0.006 PHE C 346 HIS 0.016 0.004 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01172 ( 1761) covalent geometry : angle 2.17046 ( 2355) hydrogen bonds : bond 0.17513 ( 16) hydrogen bonds : angle 6.97679 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.7438 (ptmt) cc_final: 0.6826 (ptpt) REVERT: B 321 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7606 (mttp) REVERT: B 379 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6286 (mmm-85) REVERT: C 311 LYS cc_start: 0.8273 (pttt) cc_final: 0.6798 (tppt) REVERT: C 317 LYS cc_start: 0.7407 (ptmt) cc_final: 0.7175 (ptpt) REVERT: C 321 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7746 (mttp) REVERT: C 349 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7184 (mmp-170) REVERT: C 377 THR cc_start: 0.8204 (t) cc_final: 0.7915 (p) REVERT: A 321 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8277 (mttp) REVERT: A 349 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7274 (ptt-90) REVERT: A 379 ARG cc_start: 0.7143 (ttt180) cc_final: 0.6646 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 1.2031 time to fit residues: 86.7054 Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.154383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.139048 restraints weight = 6610.432| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 2.62 r_work: 0.4563 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4466 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1761 Z= 0.166 Angle : 0.827 8.078 2355 Z= 0.441 Chirality : 0.053 0.141 264 Planarity : 0.004 0.039 300 Dihedral : 8.317 29.306 234 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.04 % Allowed : 22.22 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.40), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.016 0.003 TYR B 310 PHE 0.002 0.001 PHE B 346 HIS 0.011 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 1761) covalent geometry : angle 0.82735 ( 2355) hydrogen bonds : bond 0.04187 ( 16) hydrogen bonds : angle 6.56410 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: B 305 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.7283 (p) REVERT: B 306 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8083 (p) REVERT: B 317 LYS cc_start: 0.7586 (ptmt) cc_final: 0.6954 (ptpt) REVERT: B 379 ARG cc_start: 0.6941 (ttt180) cc_final: 0.6314 (mmm-85) REVERT: C 315 LEU cc_start: 0.8409 (tt) cc_final: 0.8137 (mp) REVERT: C 379 ARG cc_start: 0.7115 (ttt180) cc_final: 0.6299 (ttp-170) REVERT: A 306 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.7960 (m) REVERT: A 321 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8070 (mttp) REVERT: A 343 LYS cc_start: 0.8060 (tttt) cc_final: 0.7566 (mttm) REVERT: A 372 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7373 (tt0) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 0.8555 time to fit residues: 41.1518 Evaluate side-chains 32 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.164761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.150860 restraints weight = 6269.452| |-----------------------------------------------------------------------------| r_work (start): 0.4751 rms_B_bonded: 2.46 r_work: 0.4667 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4573 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1761 Z= 0.113 Angle : 0.690 5.977 2355 Z= 0.364 Chirality : 0.051 0.132 264 Planarity : 0.004 0.037 300 Dihedral : 6.843 24.467 234 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 4.55 % Allowed : 25.76 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.006 0.002 TYR B 310 PHE 0.002 0.001 PHE A 378 HIS 0.008 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 1761) covalent geometry : angle 0.68984 ( 2355) hydrogen bonds : bond 0.03549 ( 16) hydrogen bonds : angle 6.08476 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: B 305 SER cc_start: 0.7659 (OUTLIER) cc_final: 0.7452 (p) REVERT: B 306 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8161 (p) REVERT: C 315 LEU cc_start: 0.8455 (tt) cc_final: 0.8134 (mp) REVERT: C 379 ARG cc_start: 0.6917 (ttt180) cc_final: 0.6325 (ttp-170) REVERT: A 306 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8091 (m) REVERT: A 321 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8060 (mttp) REVERT: A 343 LYS cc_start: 0.8056 (tttt) cc_final: 0.7677 (mtmm) REVERT: A 372 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7746 (tt0) outliers start: 9 outliers final: 3 residues processed: 37 average time/residue: 1.1200 time to fit residues: 42.2537 Evaluate side-chains 29 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.136083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.121364 restraints weight = 7047.819| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 2.64 r_work: 0.4418 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4317 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1761 Z= 0.132 Angle : 0.668 5.477 2355 Z= 0.352 Chirality : 0.050 0.127 264 Planarity : 0.004 0.041 300 Dihedral : 6.415 23.314 234 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.03 % Allowed : 28.28 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.011 0.002 TYR C 310 PHE 0.005 0.001 PHE C 378 HIS 0.009 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 1761) covalent geometry : angle 0.66761 ( 2355) hydrogen bonds : bond 0.03462 ( 16) hydrogen bonds : angle 5.89339 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: B 305 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7318 (p) REVERT: B 306 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (p) REVERT: B 379 ARG cc_start: 0.6987 (mmm160) cc_final: 0.6426 (mmt90) REVERT: C 315 LEU cc_start: 0.8431 (tt) cc_final: 0.8206 (mp) REVERT: C 379 ARG cc_start: 0.6767 (ttt180) cc_final: 0.6211 (ttp-170) REVERT: A 306 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 321 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8077 (mttp) REVERT: A 372 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7955 (tt0) outliers start: 6 outliers final: 2 residues processed: 33 average time/residue: 1.2123 time to fit residues: 40.7366 Evaluate side-chains 24 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 0.0470 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.140910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.126177 restraints weight = 7043.846| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 2.76 r_work: 0.4486 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4384 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1761 Z= 0.101 Angle : 0.628 4.934 2355 Z= 0.323 Chirality : 0.050 0.131 264 Planarity : 0.004 0.031 300 Dihedral : 5.839 21.212 234 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.02 % Allowed : 30.81 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.010 0.002 TYR C 310 PHE 0.006 0.001 PHE A 378 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 1761) covalent geometry : angle 0.62799 ( 2355) hydrogen bonds : bond 0.03230 ( 16) hydrogen bonds : angle 5.75883 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 349 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.7007 (ttm110) REVERT: B 379 ARG cc_start: 0.7064 (mmm160) cc_final: 0.6468 (mmt90) REVERT: C 379 ARG cc_start: 0.6721 (ttt180) cc_final: 0.6055 (ttp-170) REVERT: A 306 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8186 (p) REVERT: A 372 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7961 (tt0) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 1.0545 time to fit residues: 28.0055 Evaluate side-chains 24 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain A residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.138447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.123885 restraints weight = 7019.608| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.70 r_work: 0.4460 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4361 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1761 Z= 0.109 Angle : 0.625 6.889 2355 Z= 0.320 Chirality : 0.050 0.126 264 Planarity : 0.004 0.031 300 Dihedral : 5.630 20.347 234 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.03 % Allowed : 29.80 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.48 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.010 0.002 TYR C 310 PHE 0.003 0.001 PHE A 378 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 1761) covalent geometry : angle 0.62540 ( 2355) hydrogen bonds : bond 0.02843 ( 16) hydrogen bonds : angle 5.34485 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 306 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8063 (p) REVERT: B 349 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6925 (tpp80) REVERT: B 379 ARG cc_start: 0.6977 (mmm160) cc_final: 0.6432 (mmt90) REVERT: C 315 LEU cc_start: 0.8290 (tt) cc_final: 0.8013 (mp) REVERT: C 379 ARG cc_start: 0.6766 (ttt180) cc_final: 0.6074 (ttp-170) REVERT: A 306 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8205 (p) REVERT: A 372 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7947 (tt0) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 1.2897 time to fit residues: 32.8530 Evaluate side-chains 24 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.130168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.115067 restraints weight = 7266.000| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.73 r_work: 0.4305 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4206 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1761 Z= 0.171 Angle : 0.665 4.611 2355 Z= 0.354 Chirality : 0.050 0.144 264 Planarity : 0.005 0.045 300 Dihedral : 6.103 20.807 234 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.53 % Allowed : 30.30 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.013 0.003 TYR C 310 PHE 0.005 0.001 PHE A 346 HIS 0.011 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 1761) covalent geometry : angle 0.66538 ( 2355) hydrogen bonds : bond 0.02918 ( 16) hydrogen bonds : angle 5.21525 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: B 305 SER cc_start: 0.7587 (OUTLIER) cc_final: 0.7346 (p) REVERT: B 306 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 349 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.6973 (ttm110) REVERT: B 379 ARG cc_start: 0.6979 (mmm160) cc_final: 0.6380 (mmt90) REVERT: C 379 ARG cc_start: 0.6796 (ttt180) cc_final: 0.6064 (ttp-170) REVERT: A 306 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 372 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8039 (tt0) outliers start: 5 outliers final: 1 residues processed: 22 average time/residue: 1.2997 time to fit residues: 29.1195 Evaluate side-chains 21 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.134182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.119452 restraints weight = 7378.656| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.74 r_work: 0.4366 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4268 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1761 Z= 0.122 Angle : 0.628 5.604 2355 Z= 0.326 Chirality : 0.050 0.128 264 Planarity : 0.004 0.038 300 Dihedral : 5.797 19.936 234 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.02 % Allowed : 30.81 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.87 (0.40), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.010 0.002 TYR A 310 PHE 0.003 0.001 PHE B 378 HIS 0.008 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 1761) covalent geometry : angle 0.62786 ( 2355) hydrogen bonds : bond 0.02736 ( 16) hydrogen bonds : angle 5.16305 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: B 305 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7420 (p) REVERT: B 306 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8144 (p) REVERT: B 349 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6899 (tpp80) REVERT: B 379 ARG cc_start: 0.6848 (mmm160) cc_final: 0.6343 (mmt90) REVERT: C 379 ARG cc_start: 0.6757 (ttt180) cc_final: 0.5993 (ttp-170) REVERT: A 306 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 372 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7946 (tt0) outliers start: 4 outliers final: 1 residues processed: 23 average time/residue: 1.2849 time to fit residues: 30.1358 Evaluate side-chains 23 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.135751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.121056 restraints weight = 7104.649| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 2.69 r_work: 0.4398 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4301 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1761 Z= 0.111 Angle : 0.608 5.031 2355 Z= 0.315 Chirality : 0.050 0.124 264 Planarity : 0.004 0.037 300 Dihedral : 5.626 19.705 234 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.02 % Allowed : 30.81 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.40), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.008 0.002 TYR C 310 PHE 0.003 0.001 PHE B 378 HIS 0.007 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 1761) covalent geometry : angle 0.60819 ( 2355) hydrogen bonds : bond 0.02584 ( 16) hydrogen bonds : angle 5.08906 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: B 305 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7439 (p) REVERT: B 306 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 349 ARG cc_start: 0.7109 (ttp-170) cc_final: 0.6849 (tpp80) REVERT: B 379 ARG cc_start: 0.6779 (mmm160) cc_final: 0.6289 (mmt90) REVERT: C 379 ARG cc_start: 0.6801 (ttt180) cc_final: 0.6041 (ttp-170) REVERT: A 306 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8158 (p) REVERT: A 372 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7916 (tt0) outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 1.3528 time to fit residues: 30.3004 Evaluate side-chains 24 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain A residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.136996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.122164 restraints weight = 7228.993| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 2.73 r_work: 0.4423 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4326 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1761 Z= 0.101 Angle : 0.598 4.831 2355 Z= 0.309 Chirality : 0.049 0.145 264 Planarity : 0.004 0.035 300 Dihedral : 5.484 19.872 234 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.02 % Allowed : 31.31 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.31), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.007 0.002 TYR C 310 PHE 0.003 0.001 PHE A 378 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 1761) covalent geometry : angle 0.59768 ( 2355) hydrogen bonds : bond 0.02479 ( 16) hydrogen bonds : angle 5.05265 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.106 Fit side-chains REVERT: B 306 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8111 (p) REVERT: B 349 ARG cc_start: 0.7083 (ttp-170) cc_final: 0.6836 (tpp80) REVERT: B 379 ARG cc_start: 0.6703 (mmm160) cc_final: 0.6266 (mmt90) REVERT: C 379 ARG cc_start: 0.6763 (ttt180) cc_final: 0.6039 (ttp-170) REVERT: A 306 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 372 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7927 (tt0) outliers start: 4 outliers final: 1 residues processed: 19 average time/residue: 1.5073 time to fit residues: 29.0733 Evaluate side-chains 20 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain A residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.140625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.125690 restraints weight = 6907.368| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 2.71 r_work: 0.4478 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4380 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1761 Z= 0.094 Angle : 0.569 4.831 2355 Z= 0.293 Chirality : 0.049 0.121 264 Planarity : 0.004 0.031 300 Dihedral : 5.237 18.635 234 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.03 % Allowed : 29.80 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.84 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.010 0.002 TYR A 310 PHE 0.002 0.001 PHE B 346 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 1761) covalent geometry : angle 0.56898 ( 2355) hydrogen bonds : bond 0.02426 ( 16) hydrogen bonds : angle 4.96288 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.65 seconds wall clock time: 39 minutes 4.86 seconds (2344.86 seconds total)