Starting phenix.real_space_refine on Wed Mar 12 03:15:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxi_45005/03_2025/9bxi_45005.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxi_45005/03_2025/9bxi_45005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxi_45005/03_2025/9bxi_45005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxi_45005/03_2025/9bxi_45005.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxi_45005/03_2025/9bxi_45005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxi_45005/03_2025/9bxi_45005.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 672 1.98 5 H 3654 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7182 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.81, per 1000 atoms: 0.39 Number of scatterers: 7182 At special positions: 0 Unit cell: (81.732, 159.294, 37.53, 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 6 16.00 O 672 8.00 N 648 7.00 C 2202 6.00 H 3654 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: 1.70 Conformation dependent library (CDL) restraints added in 625.1 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.506A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.422A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.807A pdb=" N SER A 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.468A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 375 Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.498A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LYS F 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.423A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340 Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.824A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER D 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.488A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 375 92 hydrogen bonds defined for protein. 276 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: 2.31 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3648 1.12 - 1.29: 600 1.29 - 1.46: 1045 1.46 - 1.63: 1937 1.63 - 1.80: 6 Bond restraints: 7236 Sorted by residual: bond pdb=" N SER D 305 " pdb=" H SER D 305 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N SER F 305 " pdb=" H SER F 305 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N SER B 305 " pdb=" H SER B 305 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LYS B 331 " pdb=" H LYS B 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LYS F 331 " pdb=" H LYS F 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 7231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11365 2.50 - 5.00: 1325 5.00 - 7.49: 474 7.49 - 9.99: 18 9.99 - 12.49: 6 Bond angle restraints: 13188 Sorted by residual: angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 118.79 -4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 118.76 -4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 118.76 -4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.74 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 118.73 -4.93 1.00e+00 1.00e+00 2.43e+01 ... (remaining 13183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 2982 13.99 - 27.97: 144 27.97 - 41.96: 72 41.96 - 55.94: 54 55.94 - 69.93: 72 Dihedral angle restraints: 3324 sinusoidal: 1902 harmonic: 1422 Sorted by residual: dihedral pdb=" CA GLN B 351 " pdb=" C GLN B 351 " pdb=" N SER B 352 " pdb=" CA SER B 352 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLN D 351 " pdb=" C GLN D 351 " pdb=" N SER D 352 " pdb=" CA SER D 352 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLN A 351 " pdb=" C GLN A 351 " pdb=" N SER A 352 " pdb=" CA SER A 352 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3321 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.053: 281 0.053 - 0.105: 163 0.105 - 0.157: 72 0.157 - 0.209: 12 0.209 - 0.261: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG D 349 " pdb=" N ARG D 349 " pdb=" C ARG D 349 " pdb=" CB ARG D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 531 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 360 " -0.020 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" N THR A 361 " 0.064 2.00e-02 2.50e+03 pdb=" CA THR A 361 " -0.018 2.00e-02 2.50e+03 pdb=" H THR A 361 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 360 " 0.020 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" N THR D 361 " -0.064 2.00e-02 2.50e+03 pdb=" CA THR D 361 " 0.018 2.00e-02 2.50e+03 pdb=" H THR D 361 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 360 " 0.020 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" N THR B 361 " -0.064 2.00e-02 2.50e+03 pdb=" CA THR B 361 " 0.018 2.00e-02 2.50e+03 pdb=" H THR B 361 " 0.025 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.40: 61 1.40 - 2.20: 778 2.20 - 3.00: 18727 3.00 - 3.80: 28293 3.80 - 4.60: 44416 Warning: very small nonbonded interaction distances. Nonbonded interactions: 92275 Sorted by model distance: nonbonded pdb=" NZ LYS B 370 " pdb=" HG SER D 316 " model vdw 0.594 2.600 nonbonded pdb=" NZ LYS C 370 " pdb=" HG SER E 316 " model vdw 0.603 2.600 nonbonded pdb=" NZ LYS D 370 " pdb=" HG SER F 316 " model vdw 0.607 2.600 nonbonded pdb=" NZ LYS A 370 " pdb=" HG SER C 316 " model vdw 0.632 2.600 nonbonded pdb=" HZ1 LYS A 370 " pdb=" HG SER C 316 " model vdw 0.734 2.100 ... (remaining 92270 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 : 0.010 0.041 3582 Z= 0.676 Angle : 1.608 5.507 4794 Z= 1.016 Chirality : 0.078 0.261 534 Planarity : 0.006 0.017 618 Dihedral : 10.278 69.928 1380 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 362 PHE 0.017 0.006 PHE E 346 TYR 0.011 0.005 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.8337 (mttt) cc_final: 0.7745 (pttt) REVERT: B 340 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8153 (mttt) REVERT: B 342 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7090 (mp0) REVERT: B 343 LYS cc_start: 0.8341 (mttt) cc_final: 0.7935 (mtpt) REVERT: C 343 LYS cc_start: 0.8212 (mttt) cc_final: 0.7972 (mtpt) REVERT: C 375 LYS cc_start: 0.8166 (tttt) cc_final: 0.7320 (ttmm) REVERT: D 338 GLU cc_start: 0.8457 (tt0) cc_final: 0.8228 (tt0) REVERT: D 343 LYS cc_start: 0.8247 (mttt) cc_final: 0.7924 (mtpm) REVERT: D 379 ARG cc_start: 0.6120 (mtt180) cc_final: 0.5746 (mmm160) REVERT: E 343 LYS cc_start: 0.8149 (mttt) cc_final: 0.7803 (mtpp) REVERT: F 340 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8003 (ttmm) REVERT: F 343 LYS cc_start: 0.8199 (mttt) cc_final: 0.7610 (tptt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 2.5175 time to fit residues: 372.1567 Evaluate side-chains 95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.167756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.131977 restraints weight = 10898.048| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.77 r_work: 0.3804 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3582 Z= 0.177 Angle : 0.581 3.603 4794 Z= 0.303 Chirality : 0.050 0.127 534 Planarity : 0.004 0.034 618 Dihedral : 6.233 19.266 480 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.49 % Allowed : 12.94 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 330 PHE 0.011 0.002 PHE A 378 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8523 (tt0) cc_final: 0.8308 (tt0) REVERT: A 340 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8175 (tmtm) REVERT: A 342 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7956 (mm-30) REVERT: B 311 LYS cc_start: 0.8389 (mttt) cc_final: 0.7733 (pttt) REVERT: B 340 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8289 (mttt) REVERT: B 342 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7144 (mp0) REVERT: B 343 LYS cc_start: 0.8606 (mttt) cc_final: 0.8157 (mtpt) REVERT: C 340 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7942 (mttt) REVERT: C 342 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7727 (mt-10) REVERT: C 343 LYS cc_start: 0.8376 (mttt) cc_final: 0.8175 (mtpt) REVERT: C 375 LYS cc_start: 0.7971 (tttt) cc_final: 0.7090 (ttmm) REVERT: D 340 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7685 (mmtm) REVERT: D 343 LYS cc_start: 0.8459 (mttt) cc_final: 0.8151 (mtpm) REVERT: E 340 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7624 (ttpp) REVERT: E 343 LYS cc_start: 0.8340 (mttt) cc_final: 0.8002 (mtpp) REVERT: F 311 LYS cc_start: 0.8376 (mttt) cc_final: 0.7672 (mttm) REVERT: F 340 LYS cc_start: 0.8240 (ttmm) cc_final: 0.8040 (ttmm) REVERT: F 343 LYS cc_start: 0.8386 (mttt) cc_final: 0.7749 (tptt) REVERT: F 372 GLU cc_start: 0.8629 (tt0) cc_final: 0.8409 (tt0) outliers start: 6 outliers final: 4 residues processed: 103 average time/residue: 2.8676 time to fit residues: 302.4687 Evaluate side-chains 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN D 368 ASN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.166183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.130905 restraints weight = 11086.593| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.76 r_work: 0.3799 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3582 Z= 0.166 Angle : 0.511 3.507 4794 Z= 0.263 Chirality : 0.050 0.129 534 Planarity : 0.004 0.039 618 Dihedral : 5.347 14.552 480 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.74 % Allowed : 17.41 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.010 0.001 PHE D 378 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8191 (tmtm) REVERT: A 342 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 311 LYS cc_start: 0.8332 (mttt) cc_final: 0.7693 (pttt) REVERT: B 314 ASP cc_start: 0.8801 (t0) cc_final: 0.8512 (t0) REVERT: B 338 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: B 340 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8294 (mttt) REVERT: B 342 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7214 (mp0) REVERT: B 343 LYS cc_start: 0.8596 (mttt) cc_final: 0.8156 (mtpt) REVERT: B 375 LYS cc_start: 0.8435 (tttt) cc_final: 0.7731 (ttmm) REVERT: C 340 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8035 (mttt) REVERT: C 342 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7739 (mt-10) REVERT: C 375 LYS cc_start: 0.8091 (tttt) cc_final: 0.7228 (ttmm) REVERT: D 340 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7650 (mmtm) REVERT: D 343 LYS cc_start: 0.8477 (mttt) cc_final: 0.8161 (mtpm) REVERT: D 369 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8473 (ttmm) REVERT: E 340 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7583 (ttpp) REVERT: E 343 LYS cc_start: 0.8335 (mttt) cc_final: 0.7988 (mtpp) REVERT: F 311 LYS cc_start: 0.8347 (mttt) cc_final: 0.7627 (mttm) REVERT: F 343 LYS cc_start: 0.8363 (mttt) cc_final: 0.7723 (tptt) outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 2.9376 time to fit residues: 289.4621 Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.166235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131438 restraints weight = 11129.661| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.77 r_work: 0.3805 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3582 Z= 0.146 Angle : 0.488 4.395 4794 Z= 0.250 Chirality : 0.049 0.126 534 Planarity : 0.004 0.038 618 Dihedral : 5.012 13.782 480 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.24 % Allowed : 19.40 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.007 0.001 PHE D 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8201 (tmtm) REVERT: A 342 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8108 (mm-30) REVERT: A 369 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8724 (ttmm) REVERT: B 311 LYS cc_start: 0.8380 (mttt) cc_final: 0.7773 (pttt) REVERT: B 314 ASP cc_start: 0.8805 (t0) cc_final: 0.8514 (t0) REVERT: B 338 GLU cc_start: 0.8550 (tt0) cc_final: 0.8323 (tm-30) REVERT: B 340 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8318 (mttt) REVERT: B 342 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7239 (mp0) REVERT: B 343 LYS cc_start: 0.8614 (mttt) cc_final: 0.8156 (mtpt) REVERT: B 375 LYS cc_start: 0.8487 (tttt) cc_final: 0.7811 (ttmm) REVERT: C 340 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8041 (mttt) REVERT: C 342 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7797 (mt-10) REVERT: D 340 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7605 (mmtm) REVERT: D 343 LYS cc_start: 0.8443 (mttt) cc_final: 0.8150 (mtpm) REVERT: E 340 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7581 (ttpp) REVERT: E 343 LYS cc_start: 0.8359 (mttt) cc_final: 0.8015 (mtpp) REVERT: F 311 LYS cc_start: 0.8367 (mttt) cc_final: 0.7671 (mttm) REVERT: F 343 LYS cc_start: 0.8428 (mttt) cc_final: 0.7751 (tptt) outliers start: 5 outliers final: 1 residues processed: 94 average time/residue: 3.0150 time to fit residues: 290.2647 Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.167405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.132628 restraints weight = 10823.529| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.76 r_work: 0.3827 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3582 Z= 0.129 Angle : 0.458 3.257 4794 Z= 0.235 Chirality : 0.049 0.126 534 Planarity : 0.004 0.038 618 Dihedral : 4.680 12.948 480 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.00 % Allowed : 18.66 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.007 0.001 PHE D 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8528 (tt0) cc_final: 0.8273 (tm-30) REVERT: A 340 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8194 (tmtm) REVERT: A 342 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8048 (mm-30) REVERT: B 311 LYS cc_start: 0.8376 (mttt) cc_final: 0.7786 (pttt) REVERT: B 338 GLU cc_start: 0.8506 (tt0) cc_final: 0.8286 (tm-30) REVERT: B 340 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8305 (mttt) REVERT: B 342 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7290 (mp0) REVERT: B 343 LYS cc_start: 0.8610 (mttt) cc_final: 0.8201 (mtpt) REVERT: B 375 LYS cc_start: 0.8508 (tttt) cc_final: 0.7827 (ttmm) REVERT: C 315 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8648 (mt) REVERT: C 340 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8061 (mttt) REVERT: C 342 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7830 (mt-10) REVERT: D 340 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7983 (mttt) REVERT: D 343 LYS cc_start: 0.8449 (mttt) cc_final: 0.8031 (mtpp) REVERT: E 340 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7613 (ttpp) REVERT: E 343 LYS cc_start: 0.8374 (mttt) cc_final: 0.7876 (mtpp) REVERT: F 311 LYS cc_start: 0.8393 (mttt) cc_final: 0.7681 (mttm) REVERT: F 343 LYS cc_start: 0.8452 (mttt) cc_final: 0.7789 (tptt) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 2.8987 time to fit residues: 279.0707 Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.167277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.132587 restraints weight = 10973.287| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.75 r_work: 0.3835 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3582 Z= 0.137 Angle : 0.457 3.448 4794 Z= 0.236 Chirality : 0.049 0.123 534 Planarity : 0.004 0.037 618 Dihedral : 4.621 13.094 480 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.74 % Allowed : 19.15 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8516 (tt0) cc_final: 0.8275 (tm-30) REVERT: A 340 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8197 (tmtm) REVERT: A 342 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 311 LYS cc_start: 0.8386 (mttt) cc_final: 0.7852 (pttt) REVERT: B 314 ASP cc_start: 0.8791 (t0) cc_final: 0.8560 (t0) REVERT: B 338 GLU cc_start: 0.8505 (tt0) cc_final: 0.8296 (tm-30) REVERT: B 340 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8301 (mttt) REVERT: B 342 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7416 (mp0) REVERT: B 343 LYS cc_start: 0.8628 (mttt) cc_final: 0.8205 (mtpt) REVERT: B 375 LYS cc_start: 0.8549 (tttt) cc_final: 0.7888 (ttmm) REVERT: C 340 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8076 (mttt) REVERT: D 340 LYS cc_start: 0.8272 (ttmm) cc_final: 0.8001 (mttt) REVERT: D 343 LYS cc_start: 0.8470 (mttt) cc_final: 0.8063 (mtpp) REVERT: E 340 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7641 (ttpp) REVERT: E 343 LYS cc_start: 0.8402 (mttt) cc_final: 0.7923 (mtpp) REVERT: E 379 ARG cc_start: 0.7472 (mmm160) cc_final: 0.7158 (mmm-85) REVERT: F 311 LYS cc_start: 0.8394 (mttt) cc_final: 0.7635 (mttm) REVERT: F 343 LYS cc_start: 0.8492 (mttt) cc_final: 0.7834 (tptt) outliers start: 7 outliers final: 2 residues processed: 94 average time/residue: 2.9107 time to fit residues: 280.5016 Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.165864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131579 restraints weight = 11036.473| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.74 r_work: 0.3811 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3582 Z= 0.136 Angle : 0.450 3.093 4794 Z= 0.232 Chirality : 0.049 0.123 534 Planarity : 0.004 0.037 618 Dihedral : 4.567 12.919 480 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.24 % Allowed : 19.40 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.008 0.002 TYR C 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8534 (tt0) cc_final: 0.8289 (tm-30) REVERT: A 340 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8168 (tmtm) REVERT: A 342 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8034 (mm-30) REVERT: B 311 LYS cc_start: 0.8390 (mttt) cc_final: 0.7832 (pttt) REVERT: B 314 ASP cc_start: 0.8796 (t0) cc_final: 0.8557 (t0) REVERT: B 340 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8289 (mttt) REVERT: B 342 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7384 (mp0) REVERT: B 343 LYS cc_start: 0.8632 (mttt) cc_final: 0.8194 (mtpt) REVERT: B 375 LYS cc_start: 0.8562 (tttt) cc_final: 0.7883 (ttmm) REVERT: C 340 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8045 (mttt) REVERT: C 342 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: C 375 LYS cc_start: 0.8229 (tttt) cc_final: 0.7416 (ttmm) REVERT: D 340 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7998 (mttt) REVERT: D 343 LYS cc_start: 0.8455 (mttt) cc_final: 0.8029 (mtpp) REVERT: E 340 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7590 (ttpp) REVERT: E 343 LYS cc_start: 0.8396 (mttt) cc_final: 0.8040 (mtpp) REVERT: E 369 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8464 (ttmt) REVERT: E 379 ARG cc_start: 0.7502 (mmm160) cc_final: 0.7212 (mmm-85) REVERT: F 311 LYS cc_start: 0.8380 (mttt) cc_final: 0.7608 (mttm) REVERT: F 343 LYS cc_start: 0.8470 (mttt) cc_final: 0.7791 (tptt) outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 2.8626 time to fit residues: 266.8679 Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.167925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133310 restraints weight = 10893.567| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.78 r_work: 0.3848 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3582 Z= 0.120 Angle : 0.439 3.816 4794 Z= 0.227 Chirality : 0.049 0.124 534 Planarity : 0.003 0.037 618 Dihedral : 4.288 12.670 480 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.75 % Allowed : 19.65 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.004 0.001 PHE D 378 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8523 (tt0) cc_final: 0.8299 (tm-30) REVERT: A 340 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8160 (tmtm) REVERT: B 311 LYS cc_start: 0.8392 (mttt) cc_final: 0.7844 (pttt) REVERT: B 314 ASP cc_start: 0.8802 (t0) cc_final: 0.8549 (t0) REVERT: B 340 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8284 (mttt) REVERT: B 342 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7389 (mp0) REVERT: B 343 LYS cc_start: 0.8598 (mttt) cc_final: 0.8189 (mtpt) REVERT: B 375 LYS cc_start: 0.8546 (tttt) cc_final: 0.7891 (ttmm) REVERT: C 306 VAL cc_start: 0.7672 (m) cc_final: 0.7467 (p) REVERT: C 340 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8042 (mttt) REVERT: C 375 LYS cc_start: 0.8231 (tttt) cc_final: 0.7429 (ttmm) REVERT: D 340 LYS cc_start: 0.8254 (ttmm) cc_final: 0.8003 (mttt) REVERT: D 343 LYS cc_start: 0.8452 (mttt) cc_final: 0.8147 (mtpm) REVERT: E 340 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7575 (ttpp) REVERT: E 343 LYS cc_start: 0.8431 (mttt) cc_final: 0.8072 (mtpp) REVERT: E 369 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8480 (ttmt) REVERT: E 379 ARG cc_start: 0.7488 (mmm160) cc_final: 0.7193 (mmm-85) REVERT: F 311 LYS cc_start: 0.8355 (mttt) cc_final: 0.7591 (mttm) REVERT: F 343 LYS cc_start: 0.8456 (mttt) cc_final: 0.7784 (tptt) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 2.9887 time to fit residues: 275.5993 Evaluate side-chains 88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.162534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.127421 restraints weight = 10938.877| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.76 r_work: 0.3762 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3582 Z= 0.202 Angle : 0.476 3.239 4794 Z= 0.247 Chirality : 0.049 0.122 534 Planarity : 0.004 0.037 618 Dihedral : 4.755 14.447 480 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.24 % Allowed : 19.40 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8534 (tt0) cc_final: 0.8308 (tm-30) REVERT: B 314 ASP cc_start: 0.8793 (t0) cc_final: 0.8547 (t0) REVERT: B 340 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8286 (mttt) REVERT: B 342 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7350 (mp0) REVERT: B 343 LYS cc_start: 0.8601 (mttt) cc_final: 0.8281 (mttm) REVERT: B 375 LYS cc_start: 0.8590 (tttt) cc_final: 0.7930 (ttmm) REVERT: C 340 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8062 (mttt) REVERT: C 342 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: C 375 LYS cc_start: 0.8220 (tttt) cc_final: 0.7431 (ttmm) REVERT: D 340 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7991 (mttt) REVERT: D 343 LYS cc_start: 0.8477 (mttt) cc_final: 0.8155 (mtpm) REVERT: E 340 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7638 (ttpp) REVERT: E 343 LYS cc_start: 0.8457 (mttt) cc_final: 0.8091 (mtpp) REVERT: E 369 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8522 (ttmt) REVERT: E 379 ARG cc_start: 0.7496 (mmm160) cc_final: 0.7186 (mmm-85) REVERT: F 311 LYS cc_start: 0.8386 (mttt) cc_final: 0.7612 (mttm) REVERT: F 343 LYS cc_start: 0.8457 (mttt) cc_final: 0.7768 (tptt) outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 3.2669 time to fit residues: 293.9817 Evaluate side-chains 87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.0050 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.164481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.129814 restraints weight = 11070.368| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.77 r_work: 0.3797 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3582 Z= 0.134 Angle : 0.452 3.403 4794 Z= 0.233 Chirality : 0.049 0.123 534 Planarity : 0.003 0.036 618 Dihedral : 4.520 13.092 480 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.75 % Allowed : 20.15 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.007 0.001 TYR D 310 ARG 0.000 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8527 (tt0) cc_final: 0.8290 (tm-30) REVERT: B 311 LYS cc_start: 0.8385 (mttt) cc_final: 0.7836 (pttt) REVERT: B 314 ASP cc_start: 0.8803 (t0) cc_final: 0.8568 (t0) REVERT: B 340 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8268 (mttt) REVERT: B 342 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7370 (mp0) REVERT: B 343 LYS cc_start: 0.8626 (mttt) cc_final: 0.8191 (mtpt) REVERT: B 375 LYS cc_start: 0.8585 (tttt) cc_final: 0.7929 (ttmm) REVERT: C 340 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8048 (mttt) REVERT: D 340 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7988 (mttt) REVERT: D 343 LYS cc_start: 0.8477 (mttt) cc_final: 0.8156 (mtpm) REVERT: E 340 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7623 (ttpp) REVERT: E 343 LYS cc_start: 0.8450 (mttt) cc_final: 0.8082 (mtpp) REVERT: E 369 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8506 (ttmt) REVERT: E 379 ARG cc_start: 0.7439 (mmm160) cc_final: 0.7155 (mmm-85) REVERT: F 311 LYS cc_start: 0.8366 (mttt) cc_final: 0.7597 (mttm) REVERT: F 343 LYS cc_start: 0.8461 (mttt) cc_final: 0.7791 (tptt) outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 4.2744 time to fit residues: 384.6488 Evaluate side-chains 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.162087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.127479 restraints weight = 11079.192| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.76 r_work: 0.3750 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3582 Z= 0.192 Angle : 0.482 3.217 4794 Z= 0.249 Chirality : 0.049 0.122 534 Planarity : 0.004 0.037 618 Dihedral : 4.854 14.818 480 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.50 % Allowed : 21.14 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.006 0.001 PHE D 378 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7861.27 seconds wall clock time: 135 minutes 32.02 seconds (8132.02 seconds total)