Starting phenix.real_space_refine on Sun Mar 10 15:15:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/03_2024/6n3b_9350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/03_2024/6n3b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/03_2024/6n3b_9350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/03_2024/6n3b_9350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/03_2024/6n3b_9350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/03_2024/6n3b_9350.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2735 Number of models: 1 Model: "" Number of chains: 10 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} Chain: "C" 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: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "E" 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: "F" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" 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: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "I" 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: "J" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Time building chain proxies: 1.76, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 525.4 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: 0.34 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: 0.61 Time building geometry restraints manager: 1.14 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: 97.72 - 104.99: 100 104.99 - 112.26: 1226 112.26 - 119.53: 904 119.53 - 126.80: 1445 126.80 - 134.06: 50 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 2.520 nonbonded pdb=" N MET A 311 " pdb=" O MET G 311 " model vdw 2.253 2.520 nonbonded pdb=" O MET E 311 " pdb=" N MET G 311 " model vdw 2.254 2.520 nonbonded pdb=" O MET A 311 " pdb=" N MET I 311 " model vdw 2.254 2.520 nonbonded pdb=" O GLN B 344 " pdb=" NE2 GLN G 331 " model vdw 2.360 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 312 through 346) selection = (chain 'B' and resid 312 through 346) selection = (chain 'C' and resid 312 through 346) selection = (chain 'D' and resid 312 through 346) selection = (chain 'E' and resid 312 through 346) selection = (chain 'F' and resid 312 through 346) selection = (chain 'G' and resid 312 through 346) selection = (chain 'H' and resid 312 through 346) selection = (chain 'I' and resid 312 through 346) selection = (chain 'J' and resid 312 through 346) } 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: 0.110 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: 0.610 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.160 Find NCS groups from input model: 0.200 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.304 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: 0.1114 time to fit residues: 16.5387 Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 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: 5.9990 chunk 20 optimal weight: 0.0670 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN B 319 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN D 319 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN I 343 GLN I 344 GLN I 346 GLN J 319 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2780 Z= 0.265 Angle : 0.834 15.637 3725 Z= 0.418 Chirality : 0.044 0.149 375 Planarity : 0.006 0.054 505 Dihedral : 6.982 22.518 375 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.77 % Allowed : 16.60 % 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: -5.26 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP J 334 PHE 0.037 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 106 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.306 Fit side-chains REVERT: B 319 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (t0) REVERT: D 316 PHE cc_start: 0.7512 (p90) cc_final: 0.6011 (m-80) REVERT: D 319 ASN cc_start: 0.8571 (p0) cc_final: 0.8306 (p0) REVERT: D 334 TRP cc_start: 0.8166 (p-90) cc_final: 0.3655 (m100) REVERT: D 337 MET cc_start: 0.7269 (ptp) cc_final: 0.5807 (mmp) REVERT: D 344 GLN cc_start: 0.7459 (pt0) cc_final: 0.7185 (tt0) REVERT: E 322 MET cc_start: 0.8378 (mtp) cc_final: 0.8157 (mtp) REVERT: F 323 MET cc_start: 0.6712 (ttp) cc_final: 0.5171 (mtt) REVERT: F 334 TRP cc_start: 0.8502 (p-90) cc_final: 0.7968 (p-90) REVERT: G 323 MET cc_start: 0.7334 (ptm) cc_final: 0.6848 (ptp) REVERT: I 323 MET cc_start: 0.7223 (ptm) cc_final: 0.6637 (ptm) REVERT: I 339 MET cc_start: 0.7498 (mpt) cc_final: 0.7178 (mpt) REVERT: I 344 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: J 313 PHE cc_start: 0.6156 (m-10) cc_final: 0.5395 (p90) REVERT: J 319 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7370 (p0) REVERT: J 323 MET cc_start: 0.5174 (ttt) cc_final: 0.4224 (mtp) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.1252 time to fit residues: 15.9200 Evaluate side-chains 92 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain H residue 340 LEU Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 344 GLN Chi-restraints excluded: chain J residue 319 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN B 319 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 344 GLN I 346 GLN J 319 ASN ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2780 Z= 0.333 Angle : 0.837 8.854 3725 Z= 0.425 Chirality : 0.046 0.162 375 Planarity : 0.006 0.055 505 Dihedral : 6.695 23.183 375 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 28.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 4.53 % Allowed : 18.49 % 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 (0.21), 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 0.028 0.003 TRP H 334 PHE 0.028 0.003 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 97 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.323 Fit side-chains REVERT: A 311 MET cc_start: 0.5311 (mtm) cc_final: 0.5020 (mtt) REVERT: D 316 PHE cc_start: 0.7619 (p90) cc_final: 0.5921 (m-80) REVERT: D 319 ASN cc_start: 0.8626 (p0) cc_final: 0.8307 (p0) REVERT: D 334 TRP cc_start: 0.7800 (p-90) cc_final: 0.4104 (m100) REVERT: D 337 MET cc_start: 0.7325 (ptp) cc_final: 0.5888 (mmp) REVERT: D 344 GLN cc_start: 0.7632 (pt0) cc_final: 0.7338 (tt0) REVERT: E 344 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: F 330 LEU cc_start: 0.7398 (pp) cc_final: 0.7000 (pp) REVERT: G 323 MET cc_start: 0.7259 (ptm) cc_final: 0.6871 (ptp) REVERT: I 323 MET cc_start: 0.7153 (ptm) cc_final: 0.6533 (ptm) REVERT: I 339 MET cc_start: 0.7653 (mpt) cc_final: 0.6977 (mpt) REVERT: I 344 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7981 (tt0) outliers start: 12 outliers final: 1 residues processed: 94 average time/residue: 0.1063 time to fit residues: 12.5662 Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 33 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 343 GLN A 346 GLN B 319 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 344 GLN I 346 GLN J 319 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2780 Z= 0.234 Angle : 0.758 8.944 3725 Z= 0.377 Chirality : 0.043 0.140 375 Planarity : 0.006 0.055 505 Dihedral : 6.159 20.380 375 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.64 % Allowed : 18.87 % Favored : 78.49 % 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 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 334 PHE 0.024 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 94 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.329 Fit side-chains REVERT: A 311 MET cc_start: 0.5102 (mtm) cc_final: 0.4887 (mtt) REVERT: C 322 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7779 (mtp) REVERT: D 316 PHE cc_start: 0.7428 (p90) cc_final: 0.5683 (m-80) REVERT: D 319 ASN cc_start: 0.8604 (p0) cc_final: 0.8250 (p0) REVERT: D 334 TRP cc_start: 0.7576 (p-90) cc_final: 0.3988 (m100) REVERT: D 337 MET cc_start: 0.7171 (ptp) cc_final: 0.5712 (mmp) REVERT: E 344 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: G 323 MET cc_start: 0.7190 (ptm) cc_final: 0.6788 (ptp) REVERT: I 323 MET cc_start: 0.6936 (ptm) cc_final: 0.6372 (ptm) REVERT: I 339 MET cc_start: 0.7517 (mpt) cc_final: 0.6744 (mpt) REVERT: I 344 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8026 (tt0) outliers start: 7 outliers final: 1 residues processed: 92 average time/residue: 0.1068 time to fit residues: 12.3224 Evaluate side-chains 85 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 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** A 346 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2780 Z= 0.284 Angle : 0.794 8.041 3725 Z= 0.389 Chirality : 0.043 0.141 375 Planarity : 0.006 0.057 505 Dihedral : 6.103 21.102 375 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 2.64 % Allowed : 21.51 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.16), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 92 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.303 Fit side-chains REVERT: A 311 MET cc_start: 0.5141 (mtm) cc_final: 0.4822 (mtt) REVERT: D 316 PHE cc_start: 0.7512 (p90) cc_final: 0.5703 (m-80) REVERT: D 319 ASN cc_start: 0.8613 (p0) cc_final: 0.8242 (p0) REVERT: D 334 TRP cc_start: 0.7628 (p-90) cc_final: 0.4100 (m100) REVERT: D 337 MET cc_start: 0.7249 (ptp) cc_final: 0.5905 (mmt) REVERT: E 344 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: G 323 MET cc_start: 0.7250 (ptm) cc_final: 0.6892 (ptp) REVERT: I 323 MET cc_start: 0.6866 (ptm) cc_final: 0.6346 (ptm) REVERT: I 344 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7996 (tt0) outliers start: 7 outliers final: 2 residues processed: 89 average time/residue: 0.1033 time to fit residues: 11.5827 Evaluate side-chains 85 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 30.0000 chunk 17 optimal weight: 40.0000 chunk 32 optimal weight: 0.0050 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 0.0050 chunk 18 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 overall best weight: 4.6014 ------------------------------------------------------------------------------- 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 ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 344 GLN I 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2780 Z= 0.236 Angle : 0.745 7.464 3725 Z= 0.368 Chirality : 0.041 0.138 375 Planarity : 0.006 0.056 505 Dihedral : 5.808 20.064 375 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.64 % Allowed : 21.89 % 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: -5.20 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.17), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 334 PHE 0.021 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 94 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.278 Fit side-chains REVERT: D 319 ASN cc_start: 0.8603 (p0) cc_final: 0.8255 (p0) REVERT: D 334 TRP cc_start: 0.7626 (p-90) cc_final: 0.4022 (m100) REVERT: D 337 MET cc_start: 0.7147 (ptp) cc_final: 0.5871 (mmt) REVERT: E 344 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: G 323 MET cc_start: 0.7216 (ptm) cc_final: 0.6801 (ptp) REVERT: H 313 PHE cc_start: 0.6345 (m-80) cc_final: 0.6081 (m-80) REVERT: H 334 TRP cc_start: 0.8613 (p-90) cc_final: 0.8365 (p-90) REVERT: I 323 MET cc_start: 0.6876 (ptm) cc_final: 0.6016 (ptt) outliers start: 7 outliers final: 2 residues processed: 92 average time/residue: 0.1066 time to fit residues: 12.3239 Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain E residue 344 GLN 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 15 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN G 319 ASN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN I 319 ASN I 346 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 2780 Z= 0.432 Angle : 0.894 9.071 3725 Z= 0.453 Chirality : 0.045 0.155 375 Planarity : 0.007 0.067 505 Dihedral : 6.539 23.010 375 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 3.02 % Allowed : 21.51 % 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: -5.30 (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 0.022 0.003 TRP J 334 PHE 0.019 0.003 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 86 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: D 319 ASN cc_start: 0.8633 (p0) cc_final: 0.8269 (p0) REVERT: D 337 MET cc_start: 0.7276 (ptp) cc_final: 0.6010 (mmt) REVERT: E 344 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: F 323 MET cc_start: 0.6828 (ttt) cc_final: 0.5184 (mtt) REVERT: G 323 MET cc_start: 0.7357 (ptm) cc_final: 0.6950 (ptm) REVERT: H 322 MET cc_start: 0.8006 (mtp) cc_final: 0.7543 (mtm) REVERT: H 334 TRP cc_start: 0.8756 (p-90) cc_final: 0.8500 (p-90) REVERT: I 323 MET cc_start: 0.7134 (ptm) cc_final: 0.6616 (ptm) outliers start: 8 outliers final: 4 residues processed: 83 average time/residue: 0.1097 time to fit residues: 11.4599 Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain H residue 316 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 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** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 343 GLN E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN H 344 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2780 Z= 0.296 Angle : 0.817 8.919 3725 Z= 0.403 Chirality : 0.043 0.149 375 Planarity : 0.006 0.064 505 Dihedral : 6.067 20.534 375 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 1.51 % Allowed : 22.64 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.17), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 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 86 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.309 Fit side-chains REVERT: D 319 ASN cc_start: 0.8590 (p0) cc_final: 0.8262 (p0) REVERT: D 337 MET cc_start: 0.7031 (ptp) cc_final: 0.5897 (mmt) REVERT: E 344 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: G 323 MET cc_start: 0.7275 (ptm) cc_final: 0.7074 (ptm) REVERT: H 334 TRP cc_start: 0.8650 (p-90) cc_final: 0.8407 (p-90) REVERT: I 323 MET cc_start: 0.7089 (ptm) cc_final: 0.6609 (ptm) outliers start: 4 outliers final: 3 residues processed: 85 average time/residue: 0.1062 time to fit residues: 11.3324 Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain G residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 319 ASN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5010 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= 0.287 Angle : 0.808 9.109 3725 Z= 0.395 Chirality : 0.043 0.152 375 Planarity : 0.006 0.067 505 Dihedral : 5.982 21.104 375 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 2.64 % Allowed : 23.40 % 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: -5.26 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.17), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 334 PHE 0.021 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 fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.326 Fit side-chains REVERT: D 319 ASN cc_start: 0.8586 (p0) cc_final: 0.8268 (p0) REVERT: D 337 MET cc_start: 0.7119 (ptp) cc_final: 0.5943 (mmt) REVERT: E 344 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: G 323 MET cc_start: 0.7247 (ptm) cc_final: 0.6862 (ptp) REVERT: H 334 TRP cc_start: 0.8660 (p-90) cc_final: 0.8396 (p-90) REVERT: I 323 MET cc_start: 0.7026 (ptm) cc_final: 0.6516 (ptm) outliers start: 7 outliers final: 3 residues processed: 84 average time/residue: 0.1098 time to fit residues: 11.6091 Evaluate side-chains 81 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain G residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 50.0000 chunk 7 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 28 optimal weight: 0.0010 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.4192 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 343 GLN G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2780 Z= 0.217 Angle : 0.733 9.091 3725 Z= 0.355 Chirality : 0.041 0.140 375 Planarity : 0.006 0.063 505 Dihedral : 5.638 18.239 375 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.13 % Allowed : 25.28 % Favored : 73.58 % 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 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.17), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 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 86 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.303 Fit side-chains REVERT: D 319 ASN cc_start: 0.8586 (p0) cc_final: 0.8279 (p0) REVERT: D 337 MET cc_start: 0.6934 (ptp) cc_final: 0.5827 (mmt) REVERT: E 344 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: G 323 MET cc_start: 0.7142 (ptm) cc_final: 0.6709 (ptp) REVERT: H 334 TRP cc_start: 0.8583 (p-90) cc_final: 0.8365 (p-90) REVERT: I 323 MET cc_start: 0.6865 (ptm) cc_final: 0.6382 (ptm) outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.1066 time to fit residues: 11.3659 Evaluate side-chains 83 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain G residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 50.0000 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.172401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.120923 restraints weight = 6042.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.124835 restraints weight = 2808.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.127273 restraints weight = 1848.519| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2780 Z= 0.288 Angle : 0.775 7.432 3725 Z= 0.382 Chirality : 0.042 0.144 375 Planarity : 0.006 0.066 505 Dihedral : 5.850 19.914 375 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Rotamer: Outliers : 1.51 % Allowed : 23.77 % Favored : 74.72 % 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: -5.25 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.17), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 334 PHE 0.020 0.002 PHE F 316 =============================================================================== Job complete usr+sys time: 858.26 seconds wall clock time: 16 minutes 18.20 seconds (978.20 seconds total)