Starting phenix.real_space_refine on Fri Dec 27 04:13:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql1_14060/12_2024/7ql1_14060.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql1_14060/12_2024/7ql1_14060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql1_14060/12_2024/7ql1_14060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql1_14060/12_2024/7ql1_14060.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql1_14060/12_2024/7ql1_14060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql1_14060/12_2024/7ql1_14060.cif" } resolution = 3.34 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1053 2.51 5 N 303 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 1671 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.83, per 1000 atoms: 1.10 Number of scatterers: 1671 At special positions: 0 Unit cell: (78.516, 85.786, 39.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 312 8.00 N 303 7.00 C 1053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 220.3 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, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.749A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.543A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 5.864A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY D 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.307A pdb=" N GLU C 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER D 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.512A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.497A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.431A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 377 removed outlier: 6.964A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 27 hydrogen bonds defined for protein. 81 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.38 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 477 1.33 - 1.45: 204 1.45 - 1.57: 1014 1.57 - 1.68: 0 1.68 - 1.80: 3 Bond restraints: 1698 Sorted by residual: bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.75e+00 bond pdb=" CB THR C 361 " pdb=" OG1 THR C 361 " ideal model delta sigma weight residual 1.433 1.389 0.044 1.60e-02 3.91e+03 7.42e+00 bond pdb=" CB THR A 361 " pdb=" OG1 THR A 361 " ideal model delta sigma weight residual 1.433 1.391 0.042 1.60e-02 3.91e+03 7.01e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.94e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.81e+00 ... (remaining 1693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 1325 1.50 - 2.99: 655 2.99 - 4.49: 215 4.49 - 5.98: 62 5.98 - 7.48: 17 Bond angle restraints: 2274 Sorted by residual: angle pdb=" CA ASP D 314 " pdb=" CB ASP D 314 " pdb=" CG ASP D 314 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " pdb=" CG ASP C 314 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 124.98 6.22 1.30e+00 5.92e-01 2.29e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 125.03 6.17 1.30e+00 5.92e-01 2.25e+01 angle pdb=" C LYS C 311 " pdb=" CA LYS C 311 " pdb=" CB LYS C 311 " ideal model delta sigma weight residual 111.11 117.00 -5.89 1.28e+00 6.10e-01 2.11e+01 ... (remaining 2269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.53: 798 8.53 - 17.06: 162 17.06 - 25.59: 42 25.59 - 34.12: 21 34.12 - 42.65: 9 Dihedral angle restraints: 1032 sinusoidal: 429 harmonic: 603 Sorted by residual: dihedral pdb=" CA ASP C 314 " pdb=" C ASP C 314 " pdb=" N LEU C 315 " pdb=" CA LEU C 315 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLN C 336 " pdb=" C GLN C 336 " pdb=" N VAL C 337 " pdb=" CA VAL C 337 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 1029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 96 0.049 - 0.097: 67 0.097 - 0.146: 50 0.146 - 0.194: 30 0.194 - 0.243: 15 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 255 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.095 2.00e-02 2.50e+03 5.25e-02 5.51e+01 pdb=" CG TYR D 310 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.073 2.00e-02 2.50e+03 4.12e-02 3.40e+01 pdb=" CG TYR C 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.058 2.00e-02 2.50e+03 2.98e-02 1.78e+01 pdb=" CG TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.039 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 1125 3.10 - 3.55: 1466 3.55 - 4.00: 2463 4.00 - 4.45: 2760 4.45 - 4.90: 4982 Nonbonded interactions: 12796 Sorted by model distance: nonbonded pdb=" N GLY A 366 " pdb=" O GLY A 366 " model vdw 2.654 2.496 nonbonded pdb=" O LEU D 325 " pdb=" CA GLY D 326 " model vdw 2.655 2.752 nonbonded pdb=" N GLY D 366 " pdb=" O GLY D 366 " model vdw 2.656 2.496 nonbonded pdb=" O PRO C 332 " pdb=" OG SER D 356 " model vdw 2.656 3.040 nonbonded pdb=" NZ LYS D 370 " pdb=" OE1 GLU D 372 " model vdw 2.663 3.120 ... (remaining 12791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.044 1698 Z= 0.722 Angle : 2.010 7.476 2274 Z= 1.340 Chirality : 0.103 0.243 258 Planarity : 0.013 0.056 288 Dihedral : 11.062 42.647 648 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: -3.09 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS C 362 PHE 0.031 0.012 PHE A 378 TYR 0.095 0.035 TYR D 310 ARG 0.003 0.001 ARG A 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 89 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.221 Fit side-chains REVERT: A 347 LYS cc_start: 0.8985 (mttt) cc_final: 0.8328 (pttm) REVERT: A 348 ASP cc_start: 0.8712 (t0) cc_final: 0.7898 (p0) REVERT: A 356 SER cc_start: 0.8863 (p) cc_final: 0.8517 (p) REVERT: C 349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7848 (mmp-170) REVERT: C 370 LYS cc_start: 0.8476 (tttt) cc_final: 0.8120 (tttt) REVERT: D 321 LYS cc_start: 0.8436 (mttt) cc_final: 0.8173 (mtpt) REVERT: D 347 LYS cc_start: 0.9016 (mttt) cc_final: 0.8763 (mptt) REVERT: D 370 LYS cc_start: 0.8664 (tttt) cc_final: 0.8380 (tttm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2843 time to fit residues: 26.8586 Evaluate side-chains 74 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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: 7.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3477 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= 0.224 Angle : 0.725 6.174 2274 Z= 0.371 Chirality : 0.052 0.146 258 Planarity : 0.004 0.035 288 Dihedral : 7.177 25.056 222 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.56 % Allowed : 17.71 % Favored : 80.73 % 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: -2.23 (0.43), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 330 PHE 0.007 0.002 PHE D 346 TYR 0.008 0.002 TYR D 310 ARG 0.004 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 77 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.195 Fit side-chains REVERT: A 347 LYS cc_start: 0.9227 (mttt) cc_final: 0.8578 (pttm) REVERT: A 348 ASP cc_start: 0.8647 (t0) cc_final: 0.7603 (p0) REVERT: A 356 SER cc_start: 0.8737 (p) cc_final: 0.8343 (p) REVERT: C 311 LYS cc_start: 0.8755 (ttmt) cc_final: 0.7955 (mmtm) REVERT: C 336 GLN cc_start: 0.8988 (mp10) cc_final: 0.8384 (mp10) REVERT: C 349 ARG cc_start: 0.8603 (mtt180) cc_final: 0.7546 (mmp-170) REVERT: D 347 LYS cc_start: 0.9078 (mttt) cc_final: 0.8799 (mptt) REVERT: D 349 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8437 (mtp85) outliers start: 3 outliers final: 0 residues processed: 75 average time/residue: 0.2333 time to fit residues: 18.8185 Evaluate side-chains 55 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1698 Z= 0.197 Angle : 0.665 5.613 2274 Z= 0.335 Chirality : 0.051 0.138 258 Planarity : 0.003 0.032 288 Dihedral : 6.195 19.800 222 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.08 % Allowed : 17.19 % Favored : 80.73 % 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 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.010 0.002 TYR D 310 ARG 0.003 0.001 ARG A 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 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.212 Fit side-chains REVERT: A 347 LYS cc_start: 0.9205 (mttt) cc_final: 0.8533 (pttm) REVERT: A 348 ASP cc_start: 0.8564 (t0) cc_final: 0.6749 (p0) REVERT: C 311 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8025 (mmtm) REVERT: C 336 GLN cc_start: 0.8364 (mp10) cc_final: 0.7545 (mm110) REVERT: C 349 ARG cc_start: 0.8669 (mtt180) cc_final: 0.7469 (mmp-170) REVERT: C 371 ILE cc_start: 0.8645 (mm) cc_final: 0.8358 (mt) REVERT: C 378 PHE cc_start: 0.7416 (m-80) cc_final: 0.7152 (m-80) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1868 time to fit residues: 11.9547 Evaluate side-chains 55 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 1698 Z= 0.414 Angle : 0.728 6.182 2274 Z= 0.371 Chirality : 0.054 0.146 258 Planarity : 0.004 0.037 288 Dihedral : 6.421 19.395 222 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.60 % Allowed : 18.23 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.010 0.002 PHE C 378 TYR 0.017 0.003 TYR D 310 ARG 0.002 0.001 ARG D 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 54 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.223 Fit side-chains REVERT: A 336 GLN cc_start: 0.8842 (mp10) cc_final: 0.8642 (tt0) REVERT: A 348 ASP cc_start: 0.8529 (t0) cc_final: 0.7685 (p0) REVERT: A 356 SER cc_start: 0.8659 (p) cc_final: 0.8138 (p) REVERT: A 368 ASN cc_start: 0.8861 (m110) cc_final: 0.8644 (m110) REVERT: C 336 GLN cc_start: 0.8859 (mp10) cc_final: 0.7716 (mm110) REVERT: C 349 ARG cc_start: 0.8852 (mtt180) cc_final: 0.7540 (mmm160) outliers start: 5 outliers final: 5 residues processed: 52 average time/residue: 0.1468 time to fit residues: 8.6956 Evaluate side-chains 50 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1698 Z= 0.162 Angle : 0.619 5.295 2274 Z= 0.312 Chirality : 0.050 0.131 258 Planarity : 0.003 0.034 288 Dihedral : 5.710 16.194 222 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -2.11 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.008 0.002 TYR D 310 ARG 0.002 0.001 ARG A 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 65 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.198 Fit side-chains REVERT: A 347 LYS cc_start: 0.9170 (mttt) cc_final: 0.8568 (pttm) REVERT: A 348 ASP cc_start: 0.8485 (t0) cc_final: 0.7399 (p0) REVERT: A 356 SER cc_start: 0.8650 (p) cc_final: 0.8134 (p) REVERT: C 311 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8066 (mmtm) REVERT: C 336 GLN cc_start: 0.8655 (mp10) cc_final: 0.7651 (mm110) REVERT: C 349 ARG cc_start: 0.8744 (mtt180) cc_final: 0.7494 (mmp-170) REVERT: C 378 PHE cc_start: 0.7576 (m-80) cc_final: 0.7358 (m-80) REVERT: D 347 LYS cc_start: 0.9015 (mttt) cc_final: 0.8782 (mptt) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.2201 time to fit residues: 15.4893 Evaluate side-chains 53 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1698 Z= 0.225 Angle : 0.639 5.509 2274 Z= 0.321 Chirality : 0.050 0.123 258 Planarity : 0.003 0.036 288 Dihedral : 5.619 16.076 222 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.52 % Allowed : 20.83 % Favored : 78.65 % 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: -2.14 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.007 0.001 PHE D 378 TYR 0.018 0.003 TYR D 310 ARG 0.002 0.001 ARG A 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 52 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.240 Fit side-chains REVERT: A 347 LYS cc_start: 0.9199 (mttt) cc_final: 0.8534 (pttm) REVERT: A 348 ASP cc_start: 0.8478 (t0) cc_final: 0.7401 (p0) REVERT: C 311 LYS cc_start: 0.8781 (ttmt) cc_final: 0.7992 (mmtm) REVERT: C 336 GLN cc_start: 0.8733 (mp10) cc_final: 0.7552 (mm110) REVERT: C 349 ARG cc_start: 0.8788 (mtt180) cc_final: 0.7695 (mmp-170) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.1877 time to fit residues: 10.9181 Evaluate side-chains 50 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1698 Z= 0.274 Angle : 0.656 5.200 2274 Z= 0.331 Chirality : 0.051 0.129 258 Planarity : 0.003 0.035 288 Dihedral : 5.693 16.446 222 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.56 % Allowed : 21.35 % Favored : 77.08 % 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: -2.24 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.007 0.001 PHE D 378 TYR 0.017 0.003 TYR D 310 ARG 0.001 0.000 ARG A 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 47 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.232 Fit side-chains REVERT: A 348 ASP cc_start: 0.8434 (t0) cc_final: 0.7325 (p0) REVERT: C 311 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8043 (mmtm) REVERT: C 336 GLN cc_start: 0.8874 (mp10) cc_final: 0.7760 (mm110) REVERT: C 349 ARG cc_start: 0.8766 (mtt180) cc_final: 0.7677 (mmp-170) outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.1608 time to fit residues: 8.4185 Evaluate side-chains 46 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1698 Z= 0.245 Angle : 0.637 5.359 2274 Z= 0.320 Chirality : 0.050 0.125 258 Planarity : 0.003 0.034 288 Dihedral : 5.604 16.204 222 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.56 % Allowed : 20.31 % Favored : 78.12 % 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: -2.32 (0.43), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.006 0.001 PHE D 378 TYR 0.016 0.003 TYR D 310 ARG 0.003 0.001 ARG D 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 49 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.234 Fit side-chains REVERT: A 348 ASP cc_start: 0.8441 (t0) cc_final: 0.7309 (p0) REVERT: A 359 ASN cc_start: 0.8672 (m110) cc_final: 0.8272 (m110) REVERT: C 311 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8022 (mmtm) REVERT: C 336 GLN cc_start: 0.8906 (mp10) cc_final: 0.7778 (mm110) REVERT: C 349 ARG cc_start: 0.8818 (mtt180) cc_final: 0.7707 (mmp-170) REVERT: D 338 GLU cc_start: 0.8152 (mp0) cc_final: 0.7897 (mp0) REVERT: D 368 ASN cc_start: 0.8952 (m-40) cc_final: 0.8711 (m110) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1617 time to fit residues: 8.8512 Evaluate side-chains 49 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1698 Z= 0.182 Angle : 0.613 5.376 2274 Z= 0.307 Chirality : 0.049 0.124 258 Planarity : 0.003 0.034 288 Dihedral : 5.342 15.045 222 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.04 % Allowed : 20.83 % Favored : 78.12 % 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: -2.40 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.006 0.001 PHE D 378 TYR 0.015 0.003 TYR D 310 ARG 0.002 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 46 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.166 Fit side-chains REVERT: A 348 ASP cc_start: 0.8481 (t0) cc_final: 0.7571 (p0) REVERT: A 349 ARG cc_start: 0.8629 (mtp85) cc_final: 0.7946 (mtm-85) REVERT: A 359 ASN cc_start: 0.8561 (m110) cc_final: 0.8135 (m110) REVERT: C 311 LYS cc_start: 0.8760 (ttmt) cc_final: 0.7975 (mmtm) REVERT: C 336 GLN cc_start: 0.8848 (mp10) cc_final: 0.7618 (mm110) REVERT: C 349 ARG cc_start: 0.8524 (mtt180) cc_final: 0.7481 (mmp-170) outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.1350 time to fit residues: 7.0022 Evaluate side-chains 44 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1698 Z= 0.206 Angle : 0.631 7.057 2274 Z= 0.317 Chirality : 0.049 0.124 258 Planarity : 0.004 0.033 288 Dihedral : 5.259 14.895 222 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.56 % Allowed : 21.35 % Favored : 77.08 % 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: -2.40 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.006 0.001 PHE D 378 TYR 0.015 0.002 TYR D 310 ARG 0.002 0.001 ARG D 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 45 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.218 Fit side-chains REVERT: A 348 ASP cc_start: 0.8550 (t0) cc_final: 0.7446 (p0) REVERT: A 349 ARG cc_start: 0.8439 (mtp85) cc_final: 0.7975 (mtm180) REVERT: A 359 ASN cc_start: 0.8534 (m110) cc_final: 0.8100 (m110) REVERT: C 311 LYS cc_start: 0.8771 (ttmt) cc_final: 0.7986 (mmtm) REVERT: C 336 GLN cc_start: 0.8830 (mp10) cc_final: 0.7630 (mm110) REVERT: C 349 ARG cc_start: 0.8536 (mtt180) cc_final: 0.7393 (mmp-170) outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.1643 time to fit residues: 8.1534 Evaluate side-chains 45 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.120498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.103813 restraints weight = 2672.597| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.90 r_work: 0.3725 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1698 Z= 0.206 Angle : 0.620 5.308 2274 Z= 0.311 Chirality : 0.050 0.124 258 Planarity : 0.004 0.039 288 Dihedral : 5.205 14.740 222 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.56 % Allowed : 21.35 % Favored : 77.08 % 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: -2.44 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.006 0.001 PHE D 378 TYR 0.015 0.003 TYR D 310 ARG 0.003 0.001 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 964.50 seconds wall clock time: 19 minutes 44.67 seconds (1184.67 seconds total)