Starting phenix.real_space_refine on Mon Feb 10 21:25:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n3b_9350/02_2025/6n3b_9350.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n3b_9350/02_2025/6n3b_9350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n3b_9350/02_2025/6n3b_9350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n3b_9350/02_2025/6n3b_9350.map" model { file = "/net/cci-nas-00/data/ceres_data/6n3b_9350/02_2025/6n3b_9350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n3b_9350/02_2025/6n3b_9350.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 55 5.16 5 C 1680 2.51 5 N 480 2.21 5 O 520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2735 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 1.25, per 1000 atoms: 0.46 Number of scatterers: 2735 At special positions: 0 Unit cell: (67.032, 82.992, 48.944, 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 55 16.00 O 520 8.00 N 480 7.00 C 1680 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: 0.64 Conformation dependent library (CDL) restraints added in 320.7 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 314 through 318 removed outlier: 6.630A pdb=" N GLY C 314 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER E 317 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 316 " --> pdb=" O SER E 317 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY E 314 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER G 317 " --> pdb=" O GLY E 314 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE E 316 " --> pdb=" O SER G 317 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 314 " --> pdb=" O ALA I 315 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER I 317 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 316 " --> pdb=" O SER I 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 321 through 322 removed outlier: 7.187A pdb=" N ALA A 321 " --> pdb=" O MET G 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 334 removed outlier: 5.591A pdb=" N ALA A 329 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER G 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN A 331 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N TRP G 334 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 333 " --> pdb=" O TRP G 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 315 through 318 removed outlier: 6.407A pdb=" N ALA B 315 " --> pdb=" O PHE H 316 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ILE H 318 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER B 317 " --> pdb=" O ILE H 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 321 through 323 removed outlier: 5.796A pdb=" N ALA B 321 " --> pdb=" O MET H 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.070A pdb=" N ALA D 328 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA F 328 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 330 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA B 328 " --> pdb=" O ALA J 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 337 through 343 removed outlier: 6.119A pdb=" N MET D 337 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU F 340 " --> pdb=" O MET D 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET D 339 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER F 342 " --> pdb=" O MET D 339 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA D 341 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET F 337 " --> pdb=" O GLY H 338 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU H 340 " --> pdb=" O MET F 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET F 339 " --> pdb=" O LEU H 340 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N SER H 342 " --> pdb=" O MET F 339 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA F 341 " --> pdb=" O SER H 342 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET B 337 " --> pdb=" O GLY J 338 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU J 340 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET B 339 " --> pdb=" O LEU J 340 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N SER J 342 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA B 341 " --> pdb=" O SER J 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 346 through 347 removed outlier: 3.514A pdb=" N SER D 347 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 347 " --> pdb=" O GLN H 346 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 346 " --> pdb=" O SER H 347 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 347 " --> pdb=" O GLN J 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 44 hydrogen bonds defined for protein. 132 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: 0.62 Time building geometry restraints manager: 0.74 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: 813 1.33 - 1.45: 450 1.45 - 1.57: 1407 1.57 - 1.69: 0 1.69 - 1.80: 110 Bond restraints: 2780 Sorted by residual: bond pdb=" CB TRP B 334 " pdb=" CG TRP B 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.18e+00 bond pdb=" CB TRP J 334 " pdb=" CG TRP J 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.15e+00 bond pdb=" CB TRP D 334 " pdb=" CG TRP D 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.13e+00 bond pdb=" CB TRP H 334 " pdb=" CG TRP H 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.12e+00 bond pdb=" CB TRP F 334 " pdb=" CG TRP F 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.12e+00 ... (remaining 2775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 3237 1.61 - 3.22: 375 3.22 - 4.83: 88 4.83 - 6.44: 15 6.44 - 8.05: 10 Bond angle restraints: 3725 Sorted by residual: angle pdb=" CA ASN B 345 " pdb=" CB ASN B 345 " pdb=" CG ASN B 345 " ideal model delta sigma weight residual 112.60 115.81 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" CA ASN F 345 " pdb=" CB ASN F 345 " pdb=" CG ASN F 345 " ideal model delta sigma weight residual 112.60 115.79 -3.19 1.00e+00 1.00e+00 1.02e+01 angle pdb=" CA ASN D 345 " pdb=" CB ASN D 345 " pdb=" CG ASN D 345 " ideal model delta sigma weight residual 112.60 115.78 -3.18 1.00e+00 1.00e+00 1.01e+01 angle pdb=" CA ASN H 345 " pdb=" CB ASN H 345 " pdb=" CG ASN H 345 " ideal model delta sigma weight residual 112.60 115.77 -3.17 1.00e+00 1.00e+00 1.00e+01 angle pdb=" CA ASN J 345 " pdb=" CB ASN J 345 " pdb=" CG ASN J 345 " ideal model delta sigma weight residual 112.60 115.76 -3.16 1.00e+00 1.00e+00 1.00e+01 ... (remaining 3720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 1520 14.12 - 28.25: 125 28.25 - 42.37: 15 42.37 - 56.49: 0 56.49 - 70.61: 5 Dihedral angle restraints: 1665 sinusoidal: 600 harmonic: 1065 Sorted by residual: dihedral pdb=" CA MET H 336 " pdb=" C MET H 336 " pdb=" N MET H 337 " pdb=" CA MET H 337 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA MET J 336 " pdb=" C MET J 336 " pdb=" N MET J 337 " pdb=" CA MET J 337 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA MET B 336 " pdb=" C MET B 336 " pdb=" N MET B 337 " pdb=" CA MET B 337 " ideal model delta harmonic sigma weight residual 180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 1662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 169 0.029 - 0.057: 108 0.057 - 0.086: 38 0.086 - 0.115: 55 0.115 - 0.143: 5 Chirality restraints: 375 Sorted by residual: chirality pdb=" CA ILE D 318 " pdb=" N ILE D 318 " pdb=" C ILE D 318 " pdb=" CB ILE D 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE J 318 " pdb=" N ILE J 318 " pdb=" C ILE J 318 " pdb=" CB ILE J 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE H 318 " pdb=" N ILE H 318 " pdb=" C ILE H 318 " pdb=" CB ILE H 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 372 not shown) Planarity restraints: 505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 348 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO H 349 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 349 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 349 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 348 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO J 349 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO J 349 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 349 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 348 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO B 349 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 349 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 349 " 0.028 5.00e-02 4.00e+02 ... (remaining 502 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 626 2.78 - 3.31: 2424 3.31 - 3.84: 4457 3.84 - 4.37: 5236 4.37 - 4.90: 9699 Nonbonded interactions: 22442 Sorted by model distance: nonbonded pdb=" O MET C 311 " pdb=" N MET E 311 " model vdw 2.253 3.120 nonbonded pdb=" N MET A 311 " pdb=" O MET G 311 " model vdw 2.253 3.120 nonbonded pdb=" O MET E 311 " pdb=" N MET G 311 " model vdw 2.254 3.120 nonbonded pdb=" O MET A 311 " pdb=" N MET I 311 " model vdw 2.254 3.120 nonbonded pdb=" O GLN B 344 " pdb=" NE2 GLN G 331 " model vdw 2.360 3.120 ... (remaining 22437 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 2780 Z= 0.672 Angle : 1.207 8.052 3725 Z= 0.650 Chirality : 0.054 0.143 375 Planarity : 0.009 0.051 505 Dihedral : 11.404 70.614 975 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -5.17 (0.24), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.18), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP D 334 PHE 0.035 0.009 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.305 Fit side-chains REVERT: B 313 PHE cc_start: 0.6918 (m-10) cc_final: 0.6592 (m-80) REVERT: B 334 TRP cc_start: 0.8783 (p-90) cc_final: 0.7830 (p-90) REVERT: B 342 SER cc_start: 0.8351 (m) cc_final: 0.8000 (p) REVERT: D 316 PHE cc_start: 0.7542 (p90) cc_final: 0.5855 (m-80) REVERT: D 334 TRP cc_start: 0.8162 (p-90) cc_final: 0.4016 (t60) REVERT: D 337 MET cc_start: 0.7292 (ptp) cc_final: 0.5921 (mmp) REVERT: D 344 GLN cc_start: 0.7142 (pt0) cc_final: 0.6919 (tt0) REVERT: E 336 MET cc_start: 0.7385 (mtt) cc_final: 0.7118 (mtt) REVERT: F 323 MET cc_start: 0.6223 (ttp) cc_final: 0.5182 (mtt) REVERT: F 334 TRP cc_start: 0.8681 (p-90) cc_final: 0.8042 (p-90) REVERT: G 323 MET cc_start: 0.7210 (ptm) cc_final: 0.6992 (ptm) REVERT: H 334 TRP cc_start: 0.8604 (p-90) cc_final: 0.8011 (p-90) REVERT: H 342 SER cc_start: 0.8294 (m) cc_final: 0.7925 (p) REVERT: I 323 MET cc_start: 0.7277 (ptm) cc_final: 0.6947 (ptm) REVERT: J 313 PHE cc_start: 0.6858 (m-10) cc_final: 0.6530 (p90) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1069 time to fit residues: 15.8398 Evaluate side-chains 82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN I 344 GLN I 346 GLN J 344 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.125594 restraints weight = 5898.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.129111 restraints weight = 3052.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.131372 restraints weight = 2028.849| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2780 Z= 0.281 Angle : 0.849 15.817 3725 Z= 0.432 Chirality : 0.045 0.157 375 Planarity : 0.007 0.054 505 Dihedral : 7.092 23.140 375 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.64 % Allowed : 17.36 % Favored : 80.00 % 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: -5.29 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 334 PHE 0.036 0.003 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: D 316 PHE cc_start: 0.7609 (p90) cc_final: 0.6078 (m-80) REVERT: D 319 ASN cc_start: 0.8463 (p0) cc_final: 0.8177 (p0) REVERT: D 334 TRP cc_start: 0.8191 (p-90) cc_final: 0.3617 (m100) REVERT: D 337 MET cc_start: 0.7297 (ptp) cc_final: 0.5881 (mmp) REVERT: D 344 GLN cc_start: 0.7453 (pt0) cc_final: 0.7202 (tt0) REVERT: F 323 MET cc_start: 0.6809 (ttp) cc_final: 0.5280 (mtt) REVERT: F 334 TRP cc_start: 0.8498 (p-90) cc_final: 0.7803 (p-90) REVERT: G 323 MET cc_start: 0.7533 (ptm) cc_final: 0.7117 (ptp) REVERT: I 323 MET cc_start: 0.7368 (ptm) cc_final: 0.6794 (ptm) REVERT: I 339 MET cc_start: 0.7486 (mpt) cc_final: 0.7178 (mpt) REVERT: J 313 PHE cc_start: 0.6116 (m-10) cc_final: 0.5231 (p90) REVERT: J 323 MET cc_start: 0.5223 (ttt) cc_final: 0.4231 (mtp) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.1056 time to fit residues: 13.6887 Evaluate side-chains 88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain H residue 340 LEU Chi-restraints excluded: chain I residue 333 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 28 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.166913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.120726 restraints weight = 5706.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.124579 restraints weight = 2786.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.126998 restraints weight = 1833.414| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2780 Z= 0.322 Angle : 0.810 9.055 3725 Z= 0.418 Chirality : 0.045 0.151 375 Planarity : 0.006 0.053 505 Dihedral : 6.691 23.683 375 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.40 % Allowed : 16.98 % Favored : 79.62 % 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: -5.24 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 334 PHE 0.027 0.002 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.312 Fit side-chains REVERT: D 316 PHE cc_start: 0.7614 (p90) cc_final: 0.5905 (m-80) REVERT: D 319 ASN cc_start: 0.8602 (p0) cc_final: 0.8309 (p0) REVERT: D 322 MET cc_start: 0.8316 (mtt) cc_final: 0.8097 (mtt) REVERT: D 334 TRP cc_start: 0.7976 (p-90) cc_final: 0.4112 (m100) REVERT: D 337 MET cc_start: 0.7462 (ptp) cc_final: 0.5924 (mmp) REVERT: D 344 GLN cc_start: 0.7571 (pt0) cc_final: 0.7224 (tt0) REVERT: E 344 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: F 323 MET cc_start: 0.6153 (ttp) cc_final: 0.4727 (mtt) REVERT: H 319 ASN cc_start: 0.8579 (p0) cc_final: 0.8355 (t0) REVERT: I 323 MET cc_start: 0.7066 (ptm) cc_final: 0.6508 (ptm) REVERT: I 339 MET cc_start: 0.7844 (mpt) cc_final: 0.7099 (mpt) outliers start: 9 outliers final: 2 residues processed: 95 average time/residue: 0.1039 time to fit residues: 12.4488 Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 344 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 40.0000 chunk 10 optimal weight: 40.0000 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.174771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.121063 restraints weight = 5717.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.124933 restraints weight = 2799.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.127331 restraints weight = 1840.722| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2780 Z= 0.287 Angle : 0.790 9.374 3725 Z= 0.398 Chirality : 0.043 0.145 375 Planarity : 0.006 0.049 505 Dihedral : 6.344 21.958 375 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.02 % Allowed : 18.11 % Favored : 78.87 % 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: -5.20 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP J 334 PHE 0.023 0.002 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.286 Fit side-chains REVERT: C 323 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6790 (ptp) REVERT: D 316 PHE cc_start: 0.7615 (p90) cc_final: 0.5709 (m-80) REVERT: D 319 ASN cc_start: 0.8622 (p0) cc_final: 0.8311 (p0) REVERT: D 334 TRP cc_start: 0.7679 (p-90) cc_final: 0.4059 (m100) REVERT: D 337 MET cc_start: 0.7368 (ptp) cc_final: 0.5927 (mmt) REVERT: E 344 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: H 319 ASN cc_start: 0.8647 (p0) cc_final: 0.8367 (t0) REVERT: I 323 MET cc_start: 0.6999 (ptm) cc_final: 0.6339 (ptm) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1063 time to fit residues: 12.6902 Evaluate side-chains 90 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 344 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.177155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.125446 restraints weight = 5821.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.129528 restraints weight = 2781.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.131822 restraints weight = 1808.940| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2780 Z= 0.252 Angle : 0.750 8.102 3725 Z= 0.375 Chirality : 0.042 0.141 375 Planarity : 0.005 0.049 505 Dihedral : 6.082 20.501 375 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 4.91 % Allowed : 17.36 % Favored : 77.74 % 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: -5.13 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 334 PHE 0.022 0.002 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.323 Fit side-chains REVERT: C 323 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7122 (ptp) REVERT: D 316 PHE cc_start: 0.7462 (p90) cc_final: 0.5627 (m-80) REVERT: D 319 ASN cc_start: 0.8577 (p0) cc_final: 0.8217 (p0) REVERT: D 334 TRP cc_start: 0.7660 (p-90) cc_final: 0.3930 (m100) REVERT: D 337 MET cc_start: 0.7286 (ptp) cc_final: 0.5888 (mmt) REVERT: D 344 GLN cc_start: 0.7139 (pt0) cc_final: 0.6924 (tt0) REVERT: E 344 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: F 323 MET cc_start: 0.6425 (ttt) cc_final: 0.4629 (mtt) REVERT: I 323 MET cc_start: 0.6715 (ptm) cc_final: 0.6217 (ptm) outliers start: 13 outliers final: 4 residues processed: 98 average time/residue: 0.1088 time to fit residues: 13.3816 Evaluate side-chains 91 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain I residue 333 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.1980 chunk 34 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** 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 = 0.4406 r_free = 0.4406 target = 0.169220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.126446 restraints weight = 5968.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.129790 restraints weight = 3235.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.131941 restraints weight = 2252.532| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2780 Z= 0.289 Angle : 0.771 8.734 3725 Z= 0.388 Chirality : 0.042 0.142 375 Planarity : 0.005 0.055 505 Dihedral : 6.149 21.031 375 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 2.64 % Allowed : 20.00 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 334 PHE 0.020 0.002 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.308 Fit side-chains REVERT: C 323 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6800 (ptp) REVERT: C 337 MET cc_start: 0.7636 (ttm) cc_final: 0.7230 (mtp) REVERT: D 319 ASN cc_start: 0.8598 (p0) cc_final: 0.8226 (p0) REVERT: D 337 MET cc_start: 0.7211 (ptp) cc_final: 0.5990 (mmt) REVERT: E 344 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: F 322 MET cc_start: 0.8535 (mtm) cc_final: 0.8301 (mtm) REVERT: F 344 GLN cc_start: 0.8350 (pt0) cc_final: 0.8126 (pt0) REVERT: I 323 MET cc_start: 0.6983 (ptm) cc_final: 0.6606 (ptm) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 0.1094 time to fit residues: 12.2027 Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain I residue 333 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN C 319 ASN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.168944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.124682 restraints weight = 5978.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.127692 restraints weight = 3357.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.129722 restraints weight = 2423.512| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2780 Z= 0.330 Angle : 0.814 7.963 3725 Z= 0.407 Chirality : 0.043 0.147 375 Planarity : 0.006 0.059 505 Dihedral : 6.240 21.340 375 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 3.02 % Allowed : 20.38 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 334 PHE 0.021 0.002 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: C 323 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7070 (ptp) REVERT: C 337 MET cc_start: 0.7971 (ttm) cc_final: 0.7727 (mtp) REVERT: D 319 ASN cc_start: 0.8661 (p0) cc_final: 0.8261 (p0) REVERT: D 337 MET cc_start: 0.7165 (ptp) cc_final: 0.5932 (mmt) REVERT: F 323 MET cc_start: 0.6415 (ttt) cc_final: 0.4938 (mtt) REVERT: H 334 TRP cc_start: 0.8820 (p-90) cc_final: 0.8510 (p-90) REVERT: I 323 MET cc_start: 0.7177 (ptm) cc_final: 0.6596 (ptm) REVERT: J 344 GLN cc_start: 0.7507 (pt0) cc_final: 0.7252 (pt0) outliers start: 8 outliers final: 1 residues processed: 85 average time/residue: 0.1083 time to fit residues: 11.6684 Evaluate side-chains 82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain G residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.171926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.121822 restraints weight = 5789.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.125776 restraints weight = 2830.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.128220 restraints weight = 1885.073| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2780 Z= 0.298 Angle : 0.792 10.195 3725 Z= 0.394 Chirality : 0.041 0.143 375 Planarity : 0.005 0.057 505 Dihedral : 6.068 20.556 375 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 1.89 % Allowed : 22.64 % Favored : 75.47 % 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: -5.26 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 334 PHE 0.021 0.002 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.276 Fit side-chains REVERT: C 323 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7015 (ptp) REVERT: C 337 MET cc_start: 0.7932 (ttm) cc_final: 0.7159 (mtp) REVERT: D 319 ASN cc_start: 0.8579 (p0) cc_final: 0.8241 (p0) REVERT: D 337 MET cc_start: 0.7149 (ptp) cc_final: 0.5915 (mmt) REVERT: H 334 TRP cc_start: 0.8809 (p-90) cc_final: 0.8490 (p-90) REVERT: I 323 MET cc_start: 0.7032 (ptm) cc_final: 0.6560 (ptm) REVERT: J 344 GLN cc_start: 0.6992 (pt0) cc_final: 0.6766 (pt0) outliers start: 5 outliers final: 2 residues processed: 83 average time/residue: 0.1086 time to fit residues: 11.4065 Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 316 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.172488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.120938 restraints weight = 5874.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.124596 restraints weight = 3019.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.126632 restraints weight = 2079.544| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2780 Z= 0.306 Angle : 0.792 11.307 3725 Z= 0.392 Chirality : 0.041 0.140 375 Planarity : 0.005 0.056 505 Dihedral : 5.976 20.905 375 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 1.89 % Allowed : 21.13 % Favored : 76.98 % 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: -5.23 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.17), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 334 PHE 0.020 0.002 PHE F 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.292 Fit side-chains REVERT: C 323 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6863 (ptp) REVERT: C 337 MET cc_start: 0.7881 (ttm) cc_final: 0.7043 (mtp) REVERT: D 319 ASN cc_start: 0.8614 (p0) cc_final: 0.8252 (p0) REVERT: D 337 MET cc_start: 0.7250 (ptp) cc_final: 0.6058 (mmt) REVERT: F 323 MET cc_start: 0.6503 (ttt) cc_final: 0.5052 (mtt) REVERT: H 334 TRP cc_start: 0.8772 (p-90) cc_final: 0.8487 (p-90) REVERT: I 323 MET cc_start: 0.7142 (ptm) cc_final: 0.6646 (ptm) outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 0.1054 time to fit residues: 11.0833 Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 316 PHE Chi-restraints excluded: chain H residue 339 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 40.0000 chunk 7 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 1 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.171040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.122738 restraints weight = 5830.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.126503 restraints weight = 2911.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.128625 restraints weight = 1973.171| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2780 Z= 0.265 Angle : 0.753 8.219 3725 Z= 0.374 Chirality : 0.041 0.138 375 Planarity : 0.005 0.058 505 Dihedral : 5.858 19.857 375 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 1.89 % Allowed : 21.51 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.17), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 334 PHE 0.022 0.002 PHE F 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.300 Fit side-chains REVERT: C 323 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6797 (ptp) REVERT: C 337 MET cc_start: 0.7845 (ttm) cc_final: 0.7035 (mtp) REVERT: D 319 ASN cc_start: 0.8648 (p0) cc_final: 0.8304 (p0) REVERT: D 337 MET cc_start: 0.7228 (ptp) cc_final: 0.6051 (mmt) REVERT: F 323 MET cc_start: 0.6417 (ttt) cc_final: 0.4959 (mtt) REVERT: H 334 TRP cc_start: 0.8782 (p-90) cc_final: 0.8486 (p-90) REVERT: H 344 GLN cc_start: 0.8095 (pt0) cc_final: 0.7886 (pt0) REVERT: I 323 MET cc_start: 0.7056 (ptm) cc_final: 0.6593 (ptm) outliers start: 5 outliers final: 2 residues processed: 85 average time/residue: 0.1036 time to fit residues: 11.1551 Evaluate side-chains 85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 339 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.179822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.123534 restraints weight = 5672.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.127589 restraints weight = 2707.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.130140 restraints weight = 1799.180| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2780 Z= 0.244 Angle : 0.740 7.854 3725 Z= 0.366 Chirality : 0.041 0.136 375 Planarity : 0.006 0.061 505 Dihedral : 5.742 19.213 375 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 1.89 % Allowed : 21.51 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 334 PHE 0.030 0.002 PHE F 316 =============================================================================== Job complete usr+sys time: 1043.43 seconds wall clock time: 19 minutes 34.87 seconds (1174.87 seconds total)