Starting phenix.real_space_refine on Mon Feb 10 19:41:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql1_14060/02_2025/7ql1_14060.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql1_14060/02_2025/7ql1_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_14060/02_2025/7ql1_14060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql1_14060/02_2025/7ql1_14060.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql1_14060/02_2025/7ql1_14060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql1_14060/02_2025/7ql1_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): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 1.58, per 1000 atoms: 0.95 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: 0.40 Conformation dependent library (CDL) restraints added in 215.1 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: 0.36 Time building geometry restraints manager: 0.47 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: 0.01 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: 0.340 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.500 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:2.650 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- 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 : 0.215 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: 0.2733 time to fit residues: 25.8354 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 : 0.218 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.130882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.114168 restraints weight = 2458.582| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.63 r_work: 0.3786 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.196 Fit side-chains REVERT: A 336 GLN cc_start: 0.8252 (mp10) cc_final: 0.8040 (mp10) REVERT: A 347 LYS cc_start: 0.9224 (mttt) cc_final: 0.8196 (pttm) REVERT: A 348 ASP cc_start: 0.8597 (t0) cc_final: 0.6914 (p0) REVERT: A 356 SER cc_start: 0.8753 (p) cc_final: 0.8153 (p) REVERT: C 311 LYS cc_start: 0.8760 (ttmt) cc_final: 0.7568 (mmtm) REVERT: C 336 GLN cc_start: 0.8606 (mp10) cc_final: 0.7744 (mp10) REVERT: C 348 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7932 (t70) REVERT: C 349 ARG cc_start: 0.7949 (mtt180) cc_final: 0.6635 (mmp-170) REVERT: C 377 THR cc_start: 0.8151 (t) cc_final: 0.7931 (p) REVERT: D 321 LYS cc_start: 0.8053 (mttt) cc_final: 0.7677 (mtpt) REVERT: D 340 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8130 (mppt) REVERT: D 342 GLU cc_start: 0.8212 (mp0) cc_final: 0.7803 (mp0) REVERT: D 347 LYS cc_start: 0.8828 (mttt) cc_final: 0.8286 (mptt) REVERT: D 349 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7370 (mtp85) outliers start: 3 outliers final: 0 residues processed: 75 average time/residue: 0.2382 time to fit residues: 19.2023 Evaluate side-chains 56 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP 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 20 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN D 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.127343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.109534 restraints weight = 2515.911| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.56 r_work: 0.3766 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1698 Z= 0.351 Angle : 0.721 6.281 2274 Z= 0.366 Chirality : 0.053 0.146 258 Planarity : 0.004 0.036 288 Dihedral : 6.575 20.953 222 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.56 % Allowed : 17.19 % 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: -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 0.008 0.002 HIS C 330 PHE 0.005 0.002 PHE C 378 TYR 0.014 0.002 TYR D 310 ARG 0.002 0.001 ARG D 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: 3 poor density : 58 time to evaluate : 0.203 Fit side-chains REVERT: A 336 GLN cc_start: 0.8382 (mp10) cc_final: 0.8159 (mp10) REVERT: A 347 LYS cc_start: 0.9135 (mttt) cc_final: 0.8304 (pttm) REVERT: A 348 ASP cc_start: 0.8655 (t0) cc_final: 0.6898 (p0) REVERT: A 353 LYS cc_start: 0.8887 (mttt) cc_final: 0.8654 (mtpt) REVERT: A 356 SER cc_start: 0.8650 (p) cc_final: 0.8023 (p) REVERT: C 311 LYS cc_start: 0.8963 (ttmt) cc_final: 0.7849 (mmtm) REVERT: C 336 GLN cc_start: 0.8234 (mp10) cc_final: 0.7019 (mm110) REVERT: C 349 ARG cc_start: 0.8135 (mtt180) cc_final: 0.6525 (mmm160) REVERT: C 371 ILE cc_start: 0.8789 (mm) cc_final: 0.8523 (mt) REVERT: D 349 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7703 (mtp85) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.1866 time to fit residues: 12.1569 Evaluate side-chains 57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.126750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.110812 restraints weight = 2488.427| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.60 r_work: 0.3797 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4145 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= 0.253 Angle : 0.650 5.587 2274 Z= 0.326 Chirality : 0.051 0.137 258 Planarity : 0.004 0.038 288 Dihedral : 6.126 18.291 222 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.12 % Allowed : 16.15 % 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: -2.15 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 330 PHE 0.004 0.001 PHE D 346 TYR 0.011 0.002 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 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.211 Fit side-chains REVERT: A 348 ASP cc_start: 0.8624 (t0) cc_final: 0.6892 (p0) REVERT: A 356 SER cc_start: 0.8446 (p) cc_final: 0.7710 (p) REVERT: C 311 LYS cc_start: 0.8826 (ttmt) cc_final: 0.7616 (mmtm) REVERT: C 336 GLN cc_start: 0.8408 (mp10) cc_final: 0.7037 (mm110) REVERT: C 338 GLU cc_start: 0.8109 (mp0) cc_final: 0.7807 (mp0) REVERT: C 348 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7842 (t70) REVERT: C 349 ARG cc_start: 0.8023 (mtt180) cc_final: 0.6447 (mmp-170) REVERT: C 378 PHE cc_start: 0.7255 (m-80) cc_final: 0.6999 (m-80) REVERT: D 338 GLU cc_start: 0.7950 (mp0) cc_final: 0.7580 (mp0) REVERT: D 349 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7722 (mtp85) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.1591 time to fit residues: 9.8371 Evaluate side-chains 56 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG 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 16 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.122324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.105256 restraints weight = 2557.027| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.51 r_work: 0.3693 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 1698 Z= 0.494 Angle : 0.739 5.550 2274 Z= 0.377 Chirality : 0.055 0.152 258 Planarity : 0.004 0.039 288 Dihedral : 6.524 19.782 222 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.60 % Allowed : 19.27 % 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: -2.35 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.011 0.002 PHE C 378 TYR 0.015 0.003 TYR D 310 ARG 0.002 0.001 ARG D 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 56 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.162 Fit side-chains REVERT: A 348 ASP cc_start: 0.8578 (t0) cc_final: 0.7156 (p0) REVERT: C 336 GLN cc_start: 0.8625 (mp10) cc_final: 0.8181 (mp10) REVERT: C 349 ARG cc_start: 0.8292 (mtt180) cc_final: 0.6692 (mmm160) REVERT: D 338 GLU cc_start: 0.8094 (mp0) cc_final: 0.7753 (mp0) REVERT: D 349 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7963 (mtp85) REVERT: D 368 ASN cc_start: 0.9241 (m-40) cc_final: 0.8855 (m-40) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.1680 time to fit residues: 10.1275 Evaluate side-chains 60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.125899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109988 restraints weight = 2548.845| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.60 r_work: 0.3778 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4624 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= 0.198 Angle : 0.622 5.456 2274 Z= 0.312 Chirality : 0.050 0.129 258 Planarity : 0.003 0.040 288 Dihedral : 5.875 17.064 222 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 21.35 % Favored : 75.52 % 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: -2.17 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.004 0.001 PHE D 346 TYR 0.011 0.002 TYR A 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 64 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.219 Fit side-chains REVERT: A 347 LYS cc_start: 0.8956 (mttt) cc_final: 0.8186 (pttm) REVERT: A 348 ASP cc_start: 0.8646 (t0) cc_final: 0.6830 (p0) REVERT: A 353 LYS cc_start: 0.8814 (mttt) cc_final: 0.8607 (mtpt) REVERT: C 311 LYS cc_start: 0.8788 (ttmt) cc_final: 0.7570 (mmtm) REVERT: C 336 GLN cc_start: 0.8464 (mp10) cc_final: 0.7031 (mm110) REVERT: C 348 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7813 (t70) REVERT: C 349 ARG cc_start: 0.8162 (mtt180) cc_final: 0.6589 (mmp-170) REVERT: D 338 GLU cc_start: 0.7943 (mp0) cc_final: 0.7510 (mp0) REVERT: D 349 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7579 (mtp85) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.1986 time to fit residues: 13.3017 Evaluate side-chains 60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 8.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.122362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.106202 restraints weight = 2535.284| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.58 r_work: 0.3731 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1698 Z= 0.298 Angle : 0.658 5.200 2274 Z= 0.333 Chirality : 0.051 0.129 258 Planarity : 0.004 0.037 288 Dihedral : 5.895 17.357 222 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.60 % Allowed : 21.35 % Favored : 76.04 % 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: -2.29 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.34), 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 0.011 0.002 TYR D 310 ARG 0.002 0.001 ARG D 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 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.206 Fit side-chains REVERT: A 347 LYS cc_start: 0.8985 (mttt) cc_final: 0.8193 (pttm) REVERT: A 348 ASP cc_start: 0.8629 (t0) cc_final: 0.6823 (p0) REVERT: A 353 LYS cc_start: 0.8843 (mttt) cc_final: 0.8619 (mtpt) REVERT: A 359 ASN cc_start: 0.9012 (m110) cc_final: 0.8068 (m110) REVERT: C 336 GLN cc_start: 0.8627 (mp10) cc_final: 0.7151 (mm110) REVERT: C 349 ARG cc_start: 0.8163 (mtt180) cc_final: 0.6634 (mmp-170) REVERT: D 349 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7530 (mtp85) REVERT: D 368 ASN cc_start: 0.9265 (m-40) cc_final: 0.8859 (m-40) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.1857 time to fit residues: 11.2734 Evaluate side-chains 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 375 LYS Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.123228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.106923 restraints weight = 2514.916| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.65 r_work: 0.3733 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4770 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= 0.271 Angle : 0.652 5.170 2274 Z= 0.331 Chirality : 0.051 0.128 258 Planarity : 0.004 0.038 288 Dihedral : 5.839 17.009 222 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 20.31 % Favored : 76.56 % 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 0.005 0.001 PHE D 346 TYR 0.010 0.002 TYR D 310 ARG 0.002 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 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.216 Fit side-chains REVERT: A 347 LYS cc_start: 0.9023 (mttt) cc_final: 0.8164 (pttm) REVERT: A 348 ASP cc_start: 0.8631 (t0) cc_final: 0.6820 (p0) REVERT: A 353 LYS cc_start: 0.8845 (mttt) cc_final: 0.8618 (mtpt) REVERT: A 359 ASN cc_start: 0.8943 (m110) cc_final: 0.7904 (m110) REVERT: C 336 GLN cc_start: 0.8679 (mp10) cc_final: 0.7268 (mm110) REVERT: C 349 ARG cc_start: 0.8176 (mtt180) cc_final: 0.6646 (mmp-170) REVERT: D 338 GLU cc_start: 0.8124 (mp0) cc_final: 0.7350 (mp0) REVERT: D 349 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7732 (mtp85) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.1996 time to fit residues: 12.1637 Evaluate side-chains 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 375 LYS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 368 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.120220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.103924 restraints weight = 2591.856| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.60 r_work: 0.3698 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 1698 Z= 0.404 Angle : 0.714 4.998 2274 Z= 0.363 Chirality : 0.053 0.135 258 Planarity : 0.004 0.042 288 Dihedral : 6.071 18.557 222 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.65 % Allowed : 22.40 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.50 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.006 0.001 PHE D 346 TYR 0.012 0.003 TYR D 310 ARG 0.003 0.001 ARG D 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 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.217 Fit side-chains REVERT: A 343 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8482 (mtpp) REVERT: A 347 LYS cc_start: 0.9013 (mttt) cc_final: 0.8184 (pttm) REVERT: A 348 ASP cc_start: 0.8556 (t0) cc_final: 0.7108 (p0) REVERT: A 353 LYS cc_start: 0.8871 (mttt) cc_final: 0.8636 (mtpt) REVERT: A 359 ASN cc_start: 0.8895 (m110) cc_final: 0.7752 (m110) REVERT: C 336 GLN cc_start: 0.8753 (mp10) cc_final: 0.8333 (mp10) REVERT: C 348 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.6780 (t70) REVERT: C 349 ARG cc_start: 0.8140 (mtt180) cc_final: 0.6480 (mmm160) REVERT: D 338 GLU cc_start: 0.8189 (mp0) cc_final: 0.7381 (mp0) REVERT: D 349 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7211 (mtp85) REVERT: D 368 ASN cc_start: 0.9188 (m-40) cc_final: 0.8713 (m110) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1917 time to fit residues: 12.4305 Evaluate side-chains 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.0070 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- 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 368 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.125099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.108507 restraints weight = 2645.864| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.74 r_work: 0.3748 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1698 Z= 0.247 Angle : 0.652 5.380 2274 Z= 0.328 Chirality : 0.051 0.126 258 Planarity : 0.004 0.046 288 Dihedral : 5.762 17.417 222 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.12 % Allowed : 23.96 % Favored : 72.92 % 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: -2.48 (0.45), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.004 0.001 PHE D 346 TYR 0.009 0.002 TYR A 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 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.214 Fit side-chains REVERT: A 343 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8386 (mtpp) REVERT: A 347 LYS cc_start: 0.9015 (mttt) cc_final: 0.8170 (pttm) REVERT: A 348 ASP cc_start: 0.8624 (t0) cc_final: 0.6829 (p0) REVERT: A 353 LYS cc_start: 0.8848 (mttt) cc_final: 0.8616 (mtpt) REVERT: A 359 ASN cc_start: 0.8893 (m110) cc_final: 0.7739 (m110) REVERT: C 336 GLN cc_start: 0.8699 (mp10) cc_final: 0.8263 (mp10) REVERT: C 348 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7853 (t70) REVERT: C 349 ARG cc_start: 0.8107 (mtt180) cc_final: 0.6532 (mmp-170) REVERT: D 338 GLU cc_start: 0.8084 (mp0) cc_final: 0.7415 (mp0) REVERT: D 349 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7611 (mtp85) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.1766 time to fit residues: 11.5475 Evaluate side-chains 61 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.120664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.104396 restraints weight = 2590.554| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.58 r_work: 0.3688 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1698 Z= 0.363 Angle : 0.696 5.597 2274 Z= 0.352 Chirality : 0.053 0.134 258 Planarity : 0.004 0.049 288 Dihedral : 5.921 18.410 222 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.65 % Allowed : 23.44 % Favored : 72.92 % 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: -2.55 (0.45), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.018 0.003 TYR A 310 ARG 0.002 0.001 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.34 seconds wall clock time: 23 minutes 41.17 seconds (1421.17 seconds total)