Starting phenix.real_space_refine on Tue Feb 11 00:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9i_18282/02_2025/8q9i_18282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9i_18282/02_2025/8q9i_18282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9i_18282/02_2025/8q9i_18282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9i_18282/02_2025/8q9i_18282.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9i_18282/02_2025/8q9i_18282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9i_18282/02_2025/8q9i_18282.cif" } resolution = 2.56 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1053 2.51 5 N 303 2.21 5 O 312 1.98 5 H 1740 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 3.31, per 1000 atoms: 0.97 Number of scatterers: 3411 At special positions: 0 Unit cell: (69.065, 98.145, 39.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 312 8.00 N 303 7.00 C 1053 6.00 H 1740 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 245.4 milliseconds 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 384 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.785A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.851A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.396A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.991A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.857A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.672A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.354A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.381A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.741A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 99 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: 1.06 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1737 1.12 - 1.29: 279 1.29 - 1.46: 486 1.46 - 1.64: 933 1.64 - 1.81: 3 Bond restraints: 3438 Sorted by residual: bond pdb=" CE1 PHE C 346 " pdb=" HE1 PHE C 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN E 336 " pdb="HE21 GLN E 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 PHE A 346 " pdb=" HE1 PHE A 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN A 327 " pdb="HD22 ASN A 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL A 337 " pdb=" H VAL A 337 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 5207 2.40 - 4.79: 812 4.79 - 7.19: 238 7.19 - 9.59: 13 9.59 - 11.99: 3 Bond angle restraints: 6273 Sorted by residual: angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 angle pdb=" CB HIS E 329 " pdb=" CG HIS E 329 " pdb=" CD2 HIS E 329 " ideal model delta sigma weight residual 131.20 125.13 6.07 1.30e+00 5.92e-01 2.18e+01 angle pdb=" C GLY C 334 " pdb=" N GLY C 335 " pdb=" CA GLY C 335 " ideal model delta sigma weight residual 120.60 125.21 -4.61 1.01e+00 9.80e-01 2.08e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 116.62 -5.93 1.33e+00 5.65e-01 1.99e+01 angle pdb=" CB HIS C 329 " pdb=" CG HIS C 329 " pdb=" CD2 HIS C 329 " ideal model delta sigma weight residual 131.20 125.41 5.79 1.30e+00 5.92e-01 1.98e+01 ... (remaining 6268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 1406 15.51 - 31.01: 85 31.01 - 46.51: 32 46.51 - 62.01: 44 62.01 - 77.51: 17 Dihedral angle restraints: 1584 sinusoidal: 903 harmonic: 681 Sorted by residual: dihedral pdb=" CA SER C 316 " pdb=" C SER C 316 " pdb=" N LYS C 317 " pdb=" CA LYS C 317 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS E 347 " pdb=" C LYS E 347 " pdb=" N ASP E 348 " pdb=" CA ASP E 348 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N THR C 361 " pdb=" CA THR C 361 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 1581 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 154 0.062 - 0.122: 68 0.122 - 0.183: 24 0.183 - 0.243: 8 0.243 - 0.304: 4 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASP E 348 " pdb=" N ASP E 348 " pdb=" C ASP E 348 " pdb=" CB ASP E 348 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 255 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 349 " 0.307 9.50e-02 1.11e+02 1.19e-01 9.29e+01 pdb=" NE ARG E 349 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG E 349 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG E 349 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG E 349 " -0.013 2.00e-02 2.50e+03 pdb="HH11 ARG E 349 " -0.140 2.00e-02 2.50e+03 pdb="HH12 ARG E 349 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG E 349 " -0.040 2.00e-02 2.50e+03 pdb="HH22 ARG E 349 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.108 2.00e-02 2.50e+03 4.95e-02 7.34e+01 pdb=" CG TYR C 310 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.107 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.089 2.00e-02 2.50e+03 4.44e-02 5.91e+01 pdb=" CG TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 270 2.18 - 2.79: 5939 2.79 - 3.39: 8984 3.39 - 4.00: 12050 4.00 - 4.60: 16883 Nonbonded interactions: 44126 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.609 2.450 nonbonded pdb=" OD2 ASP A 314 " pdb=" HZ1 LYS A 370 " model vdw 1.673 2.450 nonbonded pdb=" OD2 ASP E 314 " pdb=" HZ3 LYS E 370 " model vdw 1.717 2.450 ... (remaining 44121 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 'C' selection = chain 'E' } 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: 2.420 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: 0.070 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.120 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 0.011 0.035 1698 Z= 0.745 Angle : 1.796 6.814 2274 Z= 1.195 Chirality : 0.085 0.304 258 Planarity : 0.011 0.092 288 Dihedral : 11.444 77.511 648 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: -1.34 (0.48), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS A 330 PHE 0.047 0.014 PHE E 346 TYR 0.098 0.033 TYR C 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6613 (mtmm) REVERT: A 338 GLU cc_start: 0.7593 (tt0) cc_final: 0.7362 (mt-10) REVERT: A 342 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 321 LYS cc_start: 0.7235 (ttpt) cc_final: 0.6692 (mttp) REVERT: E 311 LYS cc_start: 0.6678 (ttpt) cc_final: 0.6345 (tmtt) REVERT: E 320 SER cc_start: 0.8128 (t) cc_final: 0.7827 (p) REVERT: E 321 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7258 (mttp) REVERT: E 336 GLN cc_start: 0.8340 (tt0) cc_final: 0.8109 (tt0) REVERT: E 342 GLU cc_start: 0.8292 (tt0) cc_final: 0.7751 (mt-10) REVERT: E 345 ASP cc_start: 0.7908 (m-30) cc_final: 0.7614 (t70) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 2.8188 time to fit residues: 214.1605 Evaluate side-chains 47 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.135302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.123755 restraints weight = 5990.369| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.57 r_work: 0.3866 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1698 Z= 0.204 Angle : 0.619 4.167 2274 Z= 0.330 Chirality : 0.051 0.160 258 Planarity : 0.003 0.019 288 Dihedral : 6.450 18.133 222 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.04 % Allowed : 15.10 % Favored : 83.85 % 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: -1.44 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.009 0.001 PHE A 346 TYR 0.005 0.001 TYR E 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7572 (tt0) cc_final: 0.7368 (mt-10) REVERT: A 342 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 342 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: E 342 GLU cc_start: 0.7870 (tt0) cc_final: 0.7516 (mt-10) REVERT: E 349 ARG cc_start: 0.5542 (pmt-80) cc_final: 0.4693 (mtp180) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 2.9919 time to fit residues: 145.5259 Evaluate side-chains 38 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.134148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.123097 restraints weight = 6011.132| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.53 r_work: 0.3844 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1698 Z= 0.219 Angle : 0.564 4.154 2274 Z= 0.295 Chirality : 0.051 0.150 258 Planarity : 0.002 0.012 288 Dihedral : 5.502 13.975 222 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.04 % Allowed : 19.27 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.008 0.002 PHE A 346 TYR 0.013 0.002 TYR E 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.281 Fit side-chains REVERT: A 342 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 311 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7910 (ttmt) REVERT: E 342 GLU cc_start: 0.7892 (tt0) cc_final: 0.7671 (mt-10) REVERT: E 347 LYS cc_start: 0.8113 (mptt) cc_final: 0.7901 (mptt) REVERT: E 349 ARG cc_start: 0.5745 (pmt-80) cc_final: 0.4833 (mtp85) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 2.5426 time to fit residues: 113.6765 Evaluate side-chains 38 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.131975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.121341 restraints weight = 6190.377| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.56 r_work: 0.3829 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1698 Z= 0.184 Angle : 0.520 3.938 2274 Z= 0.269 Chirality : 0.050 0.146 258 Planarity : 0.002 0.013 288 Dihedral : 5.099 12.819 222 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % 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: -1.54 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.007 0.002 PHE C 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.231 Fit side-chains REVERT: A 342 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7635 (mt-10) REVERT: C 311 LYS cc_start: 0.8364 (ttpt) cc_final: 0.7862 (ttmt) REVERT: C 345 ASP cc_start: 0.8069 (t70) cc_final: 0.7829 (t0) REVERT: C 347 LYS cc_start: 0.8108 (mttp) cc_final: 0.7833 (mptt) REVERT: E 345 ASP cc_start: 0.8275 (t0) cc_final: 0.8067 (t0) REVERT: E 349 ARG cc_start: 0.5630 (pmt-80) cc_final: 0.4775 (mtp85) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 2.3162 time to fit residues: 87.2511 Evaluate side-chains 36 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.132016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121765 restraints weight = 6164.384| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.48 r_work: 0.3851 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1698 Z= 0.143 Angle : 0.482 3.829 2274 Z= 0.246 Chirality : 0.050 0.142 258 Planarity : 0.002 0.013 288 Dihedral : 4.787 11.685 222 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % 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: -1.57 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.007 0.001 PHE A 346 TYR 0.008 0.001 TYR E 310 ARG 0.001 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.278 Fit side-chains REVERT: A 342 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 311 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7851 (ttmt) REVERT: C 345 ASP cc_start: 0.7963 (t70) cc_final: 0.7727 (t0) REVERT: C 347 LYS cc_start: 0.8075 (mttp) cc_final: 0.7829 (mptt) REVERT: E 349 ARG cc_start: 0.5657 (pmt-80) cc_final: 0.4797 (mtt180) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 2.2664 time to fit residues: 87.7056 Evaluate side-chains 37 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.134252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.123730 restraints weight = 6445.504| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.59 r_work: 0.3835 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1698 Z= 0.183 Angle : 0.501 4.042 2274 Z= 0.257 Chirality : 0.050 0.144 258 Planarity : 0.002 0.013 288 Dihedral : 4.728 11.797 222 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 17.19 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 330 PHE 0.005 0.001 PHE A 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.277 Fit side-chains REVERT: A 342 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7645 (mt-10) REVERT: C 311 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7808 (ttmt) REVERT: C 345 ASP cc_start: 0.8080 (t70) cc_final: 0.7851 (t0) REVERT: C 347 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7859 (mptt) REVERT: E 349 ARG cc_start: 0.5622 (pmt-80) cc_final: 0.4700 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 2.2668 time to fit residues: 90.0164 Evaluate side-chains 40 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.132125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.121616 restraints weight = 6339.563| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.55 r_work: 0.3814 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1698 Z= 0.194 Angle : 0.514 4.174 2274 Z= 0.264 Chirality : 0.050 0.144 258 Planarity : 0.002 0.013 288 Dihedral : 4.721 11.572 222 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.52 % Allowed : 16.67 % Favored : 82.81 % 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: -1.62 (0.45), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 330 PHE 0.006 0.001 PHE A 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.306 Fit side-chains REVERT: A 342 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 347 LYS cc_start: 0.8275 (mptt) cc_final: 0.8065 (mptt) REVERT: C 311 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7800 (tttt) REVERT: C 345 ASP cc_start: 0.8106 (t70) cc_final: 0.7857 (t0) REVERT: C 347 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7794 (mptt) REVERT: E 348 ASP cc_start: 0.6320 (t0) cc_final: 0.5998 (t0) REVERT: E 349 ARG cc_start: 0.5647 (pmt-80) cc_final: 0.4663 (mtt180) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 2.2936 time to fit residues: 91.1390 Evaluate side-chains 39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 9 optimal weight: 0.0030 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.128634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.118193 restraints weight = 6361.542| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.53 r_work: 0.3820 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1698 Z= 0.168 Angle : 0.500 4.181 2274 Z= 0.256 Chirality : 0.050 0.141 258 Planarity : 0.002 0.013 288 Dihedral : 4.638 11.181 222 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.52 % Allowed : 17.19 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.296 Fit side-chains REVERT: A 342 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 311 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7778 (tttt) REVERT: C 345 ASP cc_start: 0.8010 (t70) cc_final: 0.7791 (t0) REVERT: C 347 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7870 (mptt) REVERT: E 349 ARG cc_start: 0.5587 (pmt-80) cc_final: 0.4629 (mtt180) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 2.1525 time to fit residues: 85.7109 Evaluate side-chains 41 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.131448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.121229 restraints weight = 6143.831| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.47 r_work: 0.3853 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1698 Z= 0.150 Angle : 0.481 4.112 2274 Z= 0.244 Chirality : 0.050 0.140 258 Planarity : 0.002 0.013 288 Dihedral : 4.480 10.815 222 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.52 % Allowed : 17.71 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.58 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.004 0.001 PHE E 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.273 Fit side-chains REVERT: A 342 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 311 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7764 (ttmt) REVERT: C 347 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7868 (mptt) REVERT: E 349 ARG cc_start: 0.5611 (pmt-80) cc_final: 0.4687 (mtt180) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 2.1785 time to fit residues: 84.3596 Evaluate side-chains 39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.129066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118795 restraints weight = 6420.351| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.54 r_work: 0.3827 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1698 Z= 0.167 Angle : 0.494 4.184 2274 Z= 0.253 Chirality : 0.050 0.142 258 Planarity : 0.002 0.014 288 Dihedral : 4.494 10.778 222 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.52 % Allowed : 17.71 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.57 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.005 0.001 PHE A 346 TYR 0.009 0.002 TYR E 310 ARG 0.002 0.001 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.275 Fit side-chains REVERT: A 311 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7646 (tmtt) REVERT: A 342 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7599 (mt-10) REVERT: C 311 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7756 (ttmt) REVERT: C 347 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7881 (mptt) REVERT: E 349 ARG cc_start: 0.5619 (pmt-80) cc_final: 0.4681 (mtt180) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 2.1838 time to fit residues: 88.9969 Evaluate side-chains 41 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.130361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.120271 restraints weight = 6448.598| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.54 r_work: 0.3852 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1698 Z= 0.145 Angle : 0.481 4.083 2274 Z= 0.244 Chirality : 0.050 0.139 258 Planarity : 0.002 0.012 288 Dihedral : 4.389 10.668 222 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.52 % Allowed : 19.27 % Favored : 80.21 % 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: -1.55 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.004 0.001 PHE A 346 TYR 0.008 0.001 TYR E 310 ARG 0.001 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4238.35 seconds wall clock time: 74 minutes 48.30 seconds (4488.30 seconds total)