Starting phenix.real_space_refine on Fri Aug 22 13:42:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cax_16535/08_2025/8cax_16535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cax_16535/08_2025/8cax_16535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cax_16535/08_2025/8cax_16535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cax_16535/08_2025/8cax_16535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cax_16535/08_2025/8cax_16535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cax_16535/08_2025/8cax_16535.map" } resolution = 3.7 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 3444 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.64, per 1000 atoms: 0.19 Number of scatterers: 3444 At special positions: 0 Unit cell: (130.192, 119.48, 37.08, 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 6 16.00 O 642 8.00 N 636 7.00 C 2160 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: 0.28 Conformation dependent library (CDL) restraints added in 78.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.833A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.927A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 321 through 325 removed outlier: 8.973A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU E 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.439A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 346 removed outlier: 6.125A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 343 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS E 343 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.351A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 357 removed outlier: 6.131A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.833A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.927A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.728A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU C 325 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AB3, first strand: chain 'C' and resid 342 through 346 removed outlier: 6.838A pdb=" N LYS C 343 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB5, first strand: chain 'C' and resid 354 through 357 36 hydrogen bonds defined for protein. 108 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: 0.28 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 990 1.34 - 1.46: 739 1.46 - 1.58: 1763 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.311 0.043 1.10e-02 8.26e+03 1.50e+01 bond pdb=" CG HIS F 330 " pdb=" CD2 HIS F 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.49e+01 bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.48e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.312 0.042 1.10e-02 8.26e+03 1.45e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 4091 2.25 - 4.50: 481 4.50 - 6.76: 90 6.76 - 9.01: 12 9.01 - 11.26: 6 Bond angle restraints: 4680 Sorted by residual: angle pdb=" C HIS C 362 " pdb=" CA HIS C 362 " pdb=" CB HIS C 362 " ideal model delta sigma weight residual 109.84 121.10 -11.26 1.63e+00 3.76e-01 4.77e+01 angle pdb=" C HIS D 362 " pdb=" CA HIS D 362 " pdb=" CB HIS D 362 " ideal model delta sigma weight residual 109.84 121.09 -11.25 1.63e+00 3.76e-01 4.76e+01 angle pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta sigma weight residual 109.84 121.09 -11.25 1.63e+00 3.76e-01 4.76e+01 angle pdb=" C HIS B 362 " pdb=" CA HIS B 362 " pdb=" CB HIS B 362 " ideal model delta sigma weight residual 109.84 121.07 -11.23 1.63e+00 3.76e-01 4.75e+01 angle pdb=" C HIS A 362 " pdb=" CA HIS A 362 " pdb=" CB HIS A 362 " ideal model delta sigma weight residual 109.84 121.07 -11.23 1.63e+00 3.76e-01 4.75e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 1619 11.41 - 22.81: 350 22.81 - 34.21: 113 34.21 - 45.62: 42 45.62 - 57.02: 12 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 326 " pdb=" C GLY B 326 " pdb=" N ASN B 327 " pdb=" CA ASN B 327 " ideal model delta harmonic sigma weight residual 180.00 143.47 36.53 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA GLY E 326 " pdb=" C GLY E 326 " pdb=" N ASN E 327 " pdb=" CA ASN E 327 " ideal model delta harmonic sigma weight residual 180.00 143.49 36.51 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA GLY D 326 " pdb=" C GLY D 326 " pdb=" N ASN D 327 " pdb=" CA ASN D 327 " ideal model delta harmonic sigma weight residual 180.00 143.50 36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 193 0.045 - 0.089: 137 0.089 - 0.134: 99 0.134 - 0.179: 87 0.179 - 0.223: 12 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA HIS B 362 " pdb=" N HIS B 362 " pdb=" C HIS B 362 " pdb=" CB HIS B 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS E 362 " pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CB HIS E 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS D 362 " pdb=" N HIS D 362 " pdb=" C HIS D 362 " pdb=" CB HIS D 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.95e+00 pdb=" CG TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.024 2.00e-02 2.50e+03 1.57e-02 4.91e+00 pdb=" CG TYR B 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.024 2.00e-02 2.50e+03 1.56e-02 4.89e+00 pdb=" CG TYR A 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.003 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 648 2.80 - 3.32: 3342 3.32 - 3.85: 5056 3.85 - 4.37: 6045 4.37 - 4.90: 11475 Nonbonded interactions: 26566 Sorted by model distance: nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER F 316 " pdb=" NZ LYS F 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.271 3.120 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.271 3.120 ... (remaining 26561 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.550 Find NCS groups from input model: 0.010 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.009 0.043 3498 Z= 0.576 Angle : 1.646 11.259 4680 Z= 1.069 Chirality : 0.092 0.223 528 Planarity : 0.009 0.040 594 Dihedral : 14.826 57.023 1344 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.55 % Allowed : 7.58 % Favored : 87.88 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -3.97 (0.25), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 349 TYR 0.036 0.010 TYR E 310 PHE 0.015 0.003 PHE D 378 HIS 0.015 0.005 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00872 ( 3498) covalent geometry : angle 1.64637 ( 4680) hydrogen bonds : bond 0.17422 ( 36) hydrogen bonds : angle 8.12086 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.9051 (tttt) cc_final: 0.8834 (tttp) REVERT: B 310 TYR cc_start: 0.8145 (t80) cc_final: 0.7859 (t80) REVERT: B 346 PHE cc_start: 0.8797 (m-80) cc_final: 0.7887 (p90) REVERT: B 369 LYS cc_start: 0.8704 (mttt) cc_final: 0.8488 (ttmt) REVERT: C 310 TYR cc_start: 0.8172 (t80) cc_final: 0.7789 (t80) REVERT: C 345 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8054 (t0) REVERT: C 346 PHE cc_start: 0.8834 (m-80) cc_final: 0.8070 (p90) REVERT: D 349 ARG cc_start: 0.8905 (mtt180) cc_final: 0.8204 (pmt-80) REVERT: D 372 GLU cc_start: 0.8531 (tt0) cc_final: 0.8158 (mp0) REVERT: D 375 LYS cc_start: 0.9126 (tttt) cc_final: 0.8839 (tttp) REVERT: E 308 ILE cc_start: 0.9394 (mt) cc_final: 0.9117 (mp) REVERT: E 310 TYR cc_start: 0.8050 (t80) cc_final: 0.7797 (t80) REVERT: E 369 LYS cc_start: 0.8715 (mttt) cc_final: 0.8504 (ttpt) REVERT: E 372 GLU cc_start: 0.8734 (tt0) cc_final: 0.8312 (mp0) REVERT: E 375 LYS cc_start: 0.9018 (tttt) cc_final: 0.8741 (tttm) REVERT: E 378 PHE cc_start: 0.8799 (t80) cc_final: 0.8491 (t80) REVERT: F 343 LYS cc_start: 0.9041 (mttm) cc_final: 0.8678 (pttm) REVERT: F 349 ARG cc_start: 0.8745 (mtt180) cc_final: 0.7987 (ptt-90) outliers start: 18 outliers final: 6 residues processed: 189 average time/residue: 0.0716 time to fit residues: 15.4360 Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 368 ASN C 362 HIS D 330 HIS D 336 GLN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.119792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.103779 restraints weight = 8367.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.106114 restraints weight = 3861.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.107730 restraints weight = 2370.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.108928 restraints weight = 1690.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.109680 restraints weight = 1320.055| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3498 Z= 0.187 Angle : 0.747 6.416 4680 Z= 0.385 Chirality : 0.050 0.141 528 Planarity : 0.006 0.049 594 Dihedral : 7.254 45.201 476 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.04 % Allowed : 19.19 % Favored : 76.77 % 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: -3.53 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.013 0.002 TYR A 310 PHE 0.018 0.002 PHE E 346 HIS 0.007 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3498) covalent geometry : angle 0.74682 ( 4680) hydrogen bonds : bond 0.02036 ( 36) hydrogen bonds : angle 4.53768 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.9400 (tptm) cc_final: 0.8953 (mptt) REVERT: A 371 ILE cc_start: 0.8802 (mt) cc_final: 0.8563 (mp) REVERT: B 345 ASP cc_start: 0.8471 (t0) cc_final: 0.8219 (t0) REVERT: B 346 PHE cc_start: 0.8734 (m-80) cc_final: 0.7529 (p90) REVERT: B 358 ASP cc_start: 0.8379 (m-30) cc_final: 0.8096 (t0) REVERT: B 369 LYS cc_start: 0.7998 (mttt) cc_final: 0.7681 (ttmt) REVERT: C 310 TYR cc_start: 0.6341 (t80) cc_final: 0.5649 (t80) REVERT: C 331 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8349 (tttt) REVERT: C 336 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7439 (tp40) REVERT: C 345 ASP cc_start: 0.8107 (m-30) cc_final: 0.7794 (m-30) REVERT: C 346 PHE cc_start: 0.8573 (m-80) cc_final: 0.7593 (p90) REVERT: C 371 ILE cc_start: 0.8651 (mt) cc_final: 0.8167 (mp) REVERT: C 375 LYS cc_start: 0.8192 (tttm) cc_final: 0.7985 (tttm) REVERT: D 331 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8760 (ttmt) REVERT: D 372 GLU cc_start: 0.8028 (tt0) cc_final: 0.7361 (mp0) REVERT: D 376 LEU cc_start: 0.8316 (tp) cc_final: 0.7741 (tt) REVERT: E 308 ILE cc_start: 0.9078 (mt) cc_final: 0.8848 (mp) REVERT: E 310 TYR cc_start: 0.6917 (t80) cc_final: 0.5527 (t80) REVERT: E 369 LYS cc_start: 0.8082 (mttt) cc_final: 0.7751 (ttpt) REVERT: E 372 GLU cc_start: 0.8335 (tt0) cc_final: 0.7679 (mp0) REVERT: E 375 LYS cc_start: 0.8555 (tttt) cc_final: 0.8230 (tttm) REVERT: F 310 TYR cc_start: 0.5649 (OUTLIER) cc_final: 0.5215 (m-80) REVERT: F 376 LEU cc_start: 0.8435 (tp) cc_final: 0.7219 (mt) outliers start: 16 outliers final: 11 residues processed: 134 average time/residue: 0.0645 time to fit residues: 10.2983 Evaluate side-chains 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 30.0000 chunk 26 optimal weight: 0.0470 chunk 8 optimal weight: 30.0000 chunk 9 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 overall best weight: 5.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 330 HIS F 336 GLN F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.118473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.102356 restraints weight = 8233.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.104567 restraints weight = 3856.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.106231 restraints weight = 2433.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.107161 restraints weight = 1724.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.108170 restraints weight = 1385.294| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3498 Z= 0.189 Angle : 0.764 12.434 4680 Z= 0.370 Chirality : 0.050 0.140 528 Planarity : 0.005 0.046 594 Dihedral : 6.425 46.503 468 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % 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: -3.16 (0.26), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.20), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 349 TYR 0.015 0.003 TYR A 310 PHE 0.015 0.002 PHE E 378 HIS 0.006 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3498) covalent geometry : angle 0.76422 ( 4680) hydrogen bonds : bond 0.01939 ( 36) hydrogen bonds : angle 4.25432 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7895 (mp0) cc_final: 0.7243 (mp0) REVERT: B 344 LEU cc_start: 0.9210 (mp) cc_final: 0.8923 (mp) REVERT: B 345 ASP cc_start: 0.8554 (t0) cc_final: 0.8346 (t0) REVERT: B 346 PHE cc_start: 0.8797 (m-80) cc_final: 0.7506 (p90) REVERT: C 310 TYR cc_start: 0.6195 (t80) cc_final: 0.5538 (t80) REVERT: C 331 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8343 (tttt) REVERT: C 336 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7387 (tp40) REVERT: C 345 ASP cc_start: 0.8178 (m-30) cc_final: 0.7907 (m-30) REVERT: C 346 PHE cc_start: 0.8584 (m-80) cc_final: 0.7700 (p90) REVERT: C 371 ILE cc_start: 0.8741 (mt) cc_final: 0.8293 (mp) REVERT: D 372 GLU cc_start: 0.8090 (tt0) cc_final: 0.7439 (mp0) REVERT: D 376 LEU cc_start: 0.8401 (tp) cc_final: 0.7887 (tt) REVERT: E 308 ILE cc_start: 0.9036 (mt) cc_final: 0.8772 (mp) REVERT: E 310 TYR cc_start: 0.6802 (t80) cc_final: 0.5359 (t80) REVERT: E 336 GLN cc_start: 0.8385 (tm130) cc_final: 0.8114 (tm-30) REVERT: E 369 LYS cc_start: 0.8270 (mttt) cc_final: 0.7949 (ttpt) REVERT: E 372 GLU cc_start: 0.8306 (tt0) cc_final: 0.7641 (mp0) REVERT: E 375 LYS cc_start: 0.8573 (tttt) cc_final: 0.8130 (tttm) REVERT: F 310 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5216 (m-80) REVERT: F 376 LEU cc_start: 0.8395 (tp) cc_final: 0.6934 (mt) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.0459 time to fit residues: 6.5662 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.118962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.103186 restraints weight = 8368.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.105662 restraints weight = 3849.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.107300 restraints weight = 2325.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.108385 restraints weight = 1643.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.109260 restraints weight = 1293.897| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.157 Angle : 0.752 13.038 4680 Z= 0.351 Chirality : 0.050 0.136 528 Planarity : 0.005 0.046 594 Dihedral : 6.328 49.200 468 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.03 % Allowed : 22.73 % Favored : 74.24 % 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: -2.91 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.013 0.003 TYR B 310 PHE 0.003 0.001 PHE F 378 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3498) covalent geometry : angle 0.75235 ( 4680) hydrogen bonds : bond 0.01410 ( 36) hydrogen bonds : angle 4.23295 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7911 (mp0) cc_final: 0.7289 (mp0) REVERT: B 344 LEU cc_start: 0.9304 (mp) cc_final: 0.8976 (mp) REVERT: B 345 ASP cc_start: 0.8619 (t0) cc_final: 0.8334 (t0) REVERT: B 346 PHE cc_start: 0.8784 (m-80) cc_final: 0.7494 (p90) REVERT: C 336 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7380 (tp40) REVERT: C 345 ASP cc_start: 0.8214 (m-30) cc_final: 0.7939 (m-30) REVERT: C 346 PHE cc_start: 0.8520 (m-80) cc_final: 0.7634 (p90) REVERT: C 376 LEU cc_start: 0.8479 (tt) cc_final: 0.8230 (mt) REVERT: D 331 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8792 (ttmt) REVERT: D 372 GLU cc_start: 0.8093 (tt0) cc_final: 0.7494 (mp0) REVERT: E 308 ILE cc_start: 0.9025 (mt) cc_final: 0.8792 (mp) REVERT: E 369 LYS cc_start: 0.8377 (mttt) cc_final: 0.8085 (ttpt) REVERT: E 372 GLU cc_start: 0.8272 (tt0) cc_final: 0.7636 (mp0) outliers start: 12 outliers final: 11 residues processed: 113 average time/residue: 0.0436 time to fit residues: 6.2106 Evaluate side-chains 103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 359 ASN E 336 GLN F 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.114160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.097842 restraints weight = 8729.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.100124 restraints weight = 4074.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.101805 restraints weight = 2539.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.102939 restraints weight = 1823.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.103621 restraints weight = 1427.111| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.177 Angle : 0.780 15.073 4680 Z= 0.358 Chirality : 0.050 0.136 528 Planarity : 0.005 0.045 594 Dihedral : 6.343 50.272 468 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.54 % Allowed : 24.49 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.76 (0.28), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.011 0.003 TYR E 310 PHE 0.021 0.002 PHE E 378 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3498) covalent geometry : angle 0.77975 ( 4680) hydrogen bonds : bond 0.01746 ( 36) hydrogen bonds : angle 4.19201 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7828 (mp0) cc_final: 0.7156 (mp0) REVERT: B 344 LEU cc_start: 0.9309 (mp) cc_final: 0.8916 (mp) REVERT: B 345 ASP cc_start: 0.8564 (t0) cc_final: 0.8153 (t0) REVERT: B 346 PHE cc_start: 0.8903 (m-80) cc_final: 0.7623 (p90) REVERT: C 336 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7316 (tp40) REVERT: C 345 ASP cc_start: 0.8061 (m-30) cc_final: 0.7689 (m-30) REVERT: C 346 PHE cc_start: 0.8584 (m-80) cc_final: 0.7670 (p90) REVERT: D 372 GLU cc_start: 0.8160 (tt0) cc_final: 0.7573 (mp0) REVERT: E 308 ILE cc_start: 0.8951 (mt) cc_final: 0.8712 (mp) REVERT: E 336 GLN cc_start: 0.8002 (tm130) cc_final: 0.7642 (tm-30) REVERT: E 369 LYS cc_start: 0.8321 (mttt) cc_final: 0.7966 (ttpt) REVERT: E 372 GLU cc_start: 0.8276 (tt0) cc_final: 0.7575 (mp0) REVERT: F 336 GLN cc_start: 0.7870 (tm130) cc_final: 0.7547 (tm-30) outliers start: 14 outliers final: 13 residues processed: 112 average time/residue: 0.0543 time to fit residues: 7.6196 Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** 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 = 0.4294 r_free = 0.4294 target = 0.115106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.098639 restraints weight = 8648.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.100988 restraints weight = 4082.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.102637 restraints weight = 2535.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.103664 restraints weight = 1831.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.104411 restraints weight = 1467.844| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3498 Z= 0.152 Angle : 0.785 15.233 4680 Z= 0.353 Chirality : 0.049 0.139 528 Planarity : 0.005 0.041 594 Dihedral : 6.210 51.876 468 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.79 % Allowed : 24.49 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.59 (0.29), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 379 TYR 0.009 0.003 TYR C 310 PHE 0.020 0.002 PHE F 346 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3498) covalent geometry : angle 0.78474 ( 4680) hydrogen bonds : bond 0.01493 ( 36) hydrogen bonds : angle 4.10776 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7817 (mp0) cc_final: 0.7132 (mp0) REVERT: B 344 LEU cc_start: 0.9279 (mp) cc_final: 0.8855 (mp) REVERT: B 345 ASP cc_start: 0.8568 (t0) cc_final: 0.8240 (t0) REVERT: B 346 PHE cc_start: 0.8927 (m-80) cc_final: 0.7596 (p90) REVERT: C 336 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7464 (tp40) REVERT: C 345 ASP cc_start: 0.8085 (m-30) cc_final: 0.7758 (m-30) REVERT: C 346 PHE cc_start: 0.8617 (m-80) cc_final: 0.7796 (p90) REVERT: C 376 LEU cc_start: 0.8545 (tt) cc_final: 0.8178 (mt) REVERT: D 311 LYS cc_start: 0.3458 (OUTLIER) cc_final: 0.2930 (pptt) REVERT: D 372 GLU cc_start: 0.8159 (tt0) cc_final: 0.7478 (mp0) REVERT: E 336 GLN cc_start: 0.7728 (tm130) cc_final: 0.7509 (tm-30) REVERT: E 369 LYS cc_start: 0.8208 (mttt) cc_final: 0.7892 (ttpt) REVERT: E 372 GLU cc_start: 0.8267 (tt0) cc_final: 0.7561 (mp0) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.0577 time to fit residues: 7.9302 Evaluate side-chains 104 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 2.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.119952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.101626 restraints weight = 8237.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.103857 restraints weight = 4019.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.105432 restraints weight = 2590.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.106285 restraints weight = 1929.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.107045 restraints weight = 1608.813| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3498 Z= 0.129 Angle : 0.790 15.287 4680 Z= 0.349 Chirality : 0.049 0.139 528 Planarity : 0.004 0.041 594 Dihedral : 6.107 52.323 468 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.54 % Allowed : 25.51 % Favored : 70.96 % 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: -2.46 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.013 0.002 TYR C 310 PHE 0.022 0.001 PHE E 378 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3498) covalent geometry : angle 0.78991 ( 4680) hydrogen bonds : bond 0.01431 ( 36) hydrogen bonds : angle 4.14859 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7430 (mp0) REVERT: B 342 GLU cc_start: 0.7960 (mp0) cc_final: 0.7312 (mp0) REVERT: B 344 LEU cc_start: 0.9272 (mp) cc_final: 0.8873 (mp) REVERT: B 345 ASP cc_start: 0.8589 (t0) cc_final: 0.8265 (t0) REVERT: B 346 PHE cc_start: 0.8887 (m-80) cc_final: 0.7556 (p90) REVERT: C 336 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7448 (tp-100) REVERT: C 345 ASP cc_start: 0.8117 (m-30) cc_final: 0.7799 (m-30) REVERT: C 346 PHE cc_start: 0.8560 (m-80) cc_final: 0.7760 (p90) REVERT: D 311 LYS cc_start: 0.3668 (OUTLIER) cc_final: 0.3140 (pptt) REVERT: D 372 GLU cc_start: 0.8126 (tt0) cc_final: 0.7565 (mp0) REVERT: E 308 ILE cc_start: 0.8947 (mt) cc_final: 0.8702 (mp) REVERT: E 369 LYS cc_start: 0.8319 (mttt) cc_final: 0.8006 (ttpt) REVERT: E 372 GLU cc_start: 0.8282 (tt0) cc_final: 0.7556 (mp0) REVERT: F 376 LEU cc_start: 0.7385 (tt) cc_final: 0.6523 (mp) outliers start: 14 outliers final: 12 residues processed: 109 average time/residue: 0.0600 time to fit residues: 8.2759 Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.116765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.099762 restraints weight = 8699.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.102054 restraints weight = 4097.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.103716 restraints weight = 2567.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.104727 restraints weight = 1862.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.105483 restraints weight = 1497.017| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3498 Z= 0.151 Angle : 0.829 15.349 4680 Z= 0.360 Chirality : 0.049 0.138 528 Planarity : 0.005 0.038 594 Dihedral : 6.137 52.536 468 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.28 % Allowed : 26.26 % Favored : 70.45 % 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: -2.36 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.014 0.002 TYR C 310 PHE 0.022 0.002 PHE F 346 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3498) covalent geometry : angle 0.82922 ( 4680) hydrogen bonds : bond 0.01495 ( 36) hydrogen bonds : angle 4.22060 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7398 (mp0) REVERT: B 342 GLU cc_start: 0.7925 (mp0) cc_final: 0.7255 (mp0) REVERT: B 344 LEU cc_start: 0.9237 (mp) cc_final: 0.8823 (mp) REVERT: B 345 ASP cc_start: 0.8641 (t0) cc_final: 0.8285 (t0) REVERT: B 346 PHE cc_start: 0.8964 (m-80) cc_final: 0.7594 (p90) REVERT: C 336 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7368 (tp-100) REVERT: C 345 ASP cc_start: 0.8086 (m-30) cc_final: 0.7741 (m-30) REVERT: C 346 PHE cc_start: 0.8646 (m-80) cc_final: 0.7794 (p90) REVERT: C 376 LEU cc_start: 0.8537 (tt) cc_final: 0.8051 (mp) REVERT: D 311 LYS cc_start: 0.3444 (OUTLIER) cc_final: 0.2966 (pptt) REVERT: D 372 GLU cc_start: 0.8105 (tt0) cc_final: 0.7423 (mp0) REVERT: E 336 GLN cc_start: 0.8331 (tm130) cc_final: 0.8074 (tm-30) REVERT: E 369 LYS cc_start: 0.8230 (mttt) cc_final: 0.7929 (ttpt) REVERT: E 372 GLU cc_start: 0.8241 (tt0) cc_final: 0.7464 (mp0) REVERT: F 376 LEU cc_start: 0.7417 (tt) cc_final: 0.6466 (mp) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.0618 time to fit residues: 8.4113 Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.120972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.102934 restraints weight = 8174.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.104981 restraints weight = 4049.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.106487 restraints weight = 2654.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.107512 restraints weight = 1985.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.108299 restraints weight = 1620.150| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.165 Angle : 0.846 14.885 4680 Z= 0.369 Chirality : 0.050 0.139 528 Planarity : 0.005 0.041 594 Dihedral : 6.173 52.227 468 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.03 % Allowed : 26.01 % Favored : 70.96 % 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: -2.26 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.013 0.002 TYR E 310 PHE 0.023 0.002 PHE E 378 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3498) covalent geometry : angle 0.84561 ( 4680) hydrogen bonds : bond 0.01586 ( 36) hydrogen bonds : angle 4.34021 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7472 (mp0) REVERT: B 342 GLU cc_start: 0.7954 (mp0) cc_final: 0.7296 (mp0) REVERT: C 336 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7344 (tp-100) REVERT: C 345 ASP cc_start: 0.8022 (m-30) cc_final: 0.7678 (m-30) REVERT: C 346 PHE cc_start: 0.8639 (m-80) cc_final: 0.7785 (p90) REVERT: D 311 LYS cc_start: 0.3551 (OUTLIER) cc_final: 0.2967 (pptt) REVERT: D 372 GLU cc_start: 0.8119 (tt0) cc_final: 0.7466 (mp0) REVERT: E 372 GLU cc_start: 0.8228 (tt0) cc_final: 0.7536 (mp0) outliers start: 12 outliers final: 11 residues processed: 99 average time/residue: 0.0599 time to fit residues: 7.6774 Evaluate side-chains 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.122749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.106150 restraints weight = 8660.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.108449 restraints weight = 4056.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.109854 restraints weight = 2543.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.111122 restraints weight = 1898.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.111848 restraints weight = 1495.143| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.146 Angle : 0.855 14.794 4680 Z= 0.365 Chirality : 0.050 0.167 528 Planarity : 0.005 0.040 594 Dihedral : 6.115 52.302 468 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.03 % Allowed : 26.01 % Favored : 70.96 % 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: -2.15 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.012 0.002 TYR E 310 PHE 0.022 0.002 PHE F 378 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3498) covalent geometry : angle 0.85514 ( 4680) hydrogen bonds : bond 0.01423 ( 36) hydrogen bonds : angle 4.19993 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7402 (mp0) REVERT: B 342 GLU cc_start: 0.7868 (mp0) cc_final: 0.7195 (mp0) REVERT: B 345 ASP cc_start: 0.8715 (t0) cc_final: 0.8379 (t0) REVERT: B 346 PHE cc_start: 0.8971 (m-80) cc_final: 0.7543 (p90) REVERT: C 336 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7326 (tp-100) REVERT: C 345 ASP cc_start: 0.8032 (m-30) cc_final: 0.7682 (m-30) REVERT: C 346 PHE cc_start: 0.8639 (m-80) cc_final: 0.7788 (p90) REVERT: D 311 LYS cc_start: 0.3560 (OUTLIER) cc_final: 0.3051 (pptt) REVERT: D 372 GLU cc_start: 0.8089 (tt0) cc_final: 0.7475 (mp0) REVERT: E 372 GLU cc_start: 0.8238 (tt0) cc_final: 0.7493 (mp0) REVERT: F 311 LYS cc_start: 0.3851 (OUTLIER) cc_final: 0.3084 (pptt) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.0469 time to fit residues: 6.4871 Evaluate side-chains 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.120453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.104529 restraints weight = 8795.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.106748 restraints weight = 4149.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.108346 restraints weight = 2599.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.109285 restraints weight = 1886.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.110075 restraints weight = 1519.057| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.164 Angle : 0.872 14.748 4680 Z= 0.377 Chirality : 0.050 0.137 528 Planarity : 0.005 0.040 594 Dihedral : 6.179 51.920 468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.03 % Allowed : 26.77 % Favored : 70.20 % 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: -2.19 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 379 TYR 0.014 0.002 TYR E 310 PHE 0.023 0.002 PHE E 378 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3498) covalent geometry : angle 0.87203 ( 4680) hydrogen bonds : bond 0.01645 ( 36) hydrogen bonds : angle 4.30083 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 789.27 seconds wall clock time: 14 minutes 27.73 seconds (867.73 seconds total)