Starting phenix.real_space_refine on Fri Aug 2 17:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/08_2024/8wlj_37621.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/08_2024/8wlj_37621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/08_2024/8wlj_37621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/08_2024/8wlj_37621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/08_2024/8wlj_37621.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/08_2024/8wlj_37621.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 36 5.16 5 C 2626 2.51 5 N 662 2.21 5 O 711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4035 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3106 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 23, 'TRANS': 385} Chain breaks: 1 Chain: "D" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 3.11, per 1000 atoms: 0.77 Number of scatterers: 4035 At special positions: 0 Unit cell: (82.948, 81.084, 103.452, 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 36 16.00 O 711 8.00 N 662 7.00 C 2626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 100 " distance=2.04 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: 1.76 Conformation dependent library (CDL) restraints added in 747.8 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 958 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 73.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 3.840A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 124 through 157 removed outlier: 4.784A pdb=" N VAL A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.939A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.566A pdb=" N ILE A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 4.007A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 Proline residue: A 236 - end of helix removed outlier: 3.730A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.713A pdb=" N VAL A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.601A pdb=" N LEU A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.926A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 3.774A pdb=" N CYS A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 356 removed outlier: 4.167A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 3.659A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 378 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.252A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 4.408A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 removed outlier: 4.022A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.537A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'D' and resid 30 through 37 Processing helix chain 'D' and resid 91 through 95 removed outlier: 4.044A pdb=" N THR D 95 " --> pdb=" O PRO D 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 7 through 9 removed outlier: 3.542A pdb=" N SER D 23 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.922A pdb=" N GLY D 12 " --> pdb=" O GLN D 119 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR D 121 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL D 14 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS D 101 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 54 " --> pdb=" O TRP D 41 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 634 1.31 - 1.44: 1083 1.44 - 1.56: 2344 1.56 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 4123 Sorted by residual: bond pdb=" CA ALA A 177 " pdb=" C ALA A 177 " ideal model delta sigma weight residual 1.524 1.424 0.101 1.29e-02 6.01e+03 6.09e+01 bond pdb=" CA PHE A 176 " pdb=" C PHE A 176 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.30e-02 5.92e+03 3.02e+01 bond pdb=" CA ALA A 177 " pdb=" CB ALA A 177 " ideal model delta sigma weight residual 1.530 1.452 0.078 1.63e-02 3.76e+03 2.28e+01 bond pdb=" C PHE A 176 " pdb=" O PHE A 176 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.17e-02 7.31e+03 2.04e+01 bond pdb=" CA PHE A 178 " pdb=" C PHE A 178 " ideal model delta sigma weight residual 1.522 1.460 0.062 1.41e-02 5.03e+03 1.92e+01 ... (remaining 4118 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.17: 111 105.17 - 112.39: 2061 112.39 - 119.61: 1382 119.61 - 126.83: 1989 126.83 - 134.05: 52 Bond angle restraints: 5595 Sorted by residual: angle pdb=" N PHE A 178 " pdb=" CA PHE A 178 " pdb=" C PHE A 178 " ideal model delta sigma weight residual 112.38 101.87 10.51 1.22e+00 6.72e-01 7.42e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 110.24 119.75 -9.51 1.41e+00 5.03e-01 4.55e+01 angle pdb=" C SER A 179 " pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta sigma weight residual 109.70 101.57 8.13 1.61e+00 3.86e-01 2.55e+01 angle pdb=" C PHE A 176 " pdb=" N ALA A 177 " pdb=" CA ALA A 177 " ideal model delta sigma weight residual 120.71 114.49 6.22 1.67e+00 3.59e-01 1.39e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.34 118.79 -6.45 2.04e+00 2.40e-01 1.00e+01 ... (remaining 5590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2201 17.97 - 35.93: 200 35.93 - 53.89: 32 53.89 - 71.86: 4 71.86 - 89.82: 4 Dihedral angle restraints: 2441 sinusoidal: 938 harmonic: 1503 Sorted by residual: dihedral pdb=" C SER A 179 " pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta harmonic sigma weight residual -122.60 -113.09 -9.51 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" CA MET D 82 " pdb=" C MET D 82 " pdb=" N VAL D 83 " pdb=" CA VAL D 83 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLU D 58 " pdb=" C GLU D 58 " pdb=" N ARG D 59 " pdb=" CA ARG D 59 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 2438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 589 0.084 - 0.168: 58 0.168 - 0.252: 2 0.252 - 0.335: 0 0.335 - 0.419: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA ALA A 177 " pdb=" N ALA A 177 " pdb=" C ALA A 177 " pdb=" CB ALA A 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA MET A 175 " pdb=" N MET A 175 " pdb=" C MET A 175 " pdb=" CB MET A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 447 " pdb=" N ILE A 447 " pdb=" C ILE A 447 " pdb=" CB ILE A 447 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 647 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 174 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE A 174 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE A 174 " -0.021 2.00e-02 2.50e+03 pdb=" N MET A 175 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 175 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C MET A 175 " 0.050 2.00e-02 2.50e+03 pdb=" O MET A 175 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 176 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 312 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 313 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.033 5.00e-02 4.00e+02 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1083 2.81 - 3.33: 4121 3.33 - 3.85: 6494 3.85 - 4.38: 7142 4.38 - 4.90: 12510 Nonbonded interactions: 31350 Sorted by model distance: nonbonded pdb=" NH1 ARG D 71 " pdb=" O ASN D 89 " model vdw 2.283 3.120 nonbonded pdb=" NH1 ARG D 50 " pdb=" O VAL D 51 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG A 413 " pdb=" OE2 GLU A 479 " model vdw 2.323 3.120 nonbonded pdb=" O ILE A 301 " pdb=" ND2 ASN A 305 " model vdw 2.337 3.120 nonbonded pdb=" OE2 GLU D 8 " pdb=" N GLY D 117 " model vdw 2.343 3.120 ... (remaining 31345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.520 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.110 Find NCS groups from input model: 0.040 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.005 0.101 4123 Z= 0.314 Angle : 0.817 10.510 5595 Z= 0.431 Chirality : 0.050 0.419 650 Planarity : 0.006 0.073 702 Dihedral : 14.045 89.824 1480 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.21 % 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: 0.69 (0.36), residues: 524 helix: 1.05 (0.27), residues: 345 sheet: 0.34 (0.89), residues: 42 loop : -0.87 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.026 0.002 PHE A 334 TYR 0.017 0.002 TYR A 422 ARG 0.006 0.001 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7930 (mm-30) REVERT: A 142 GLN cc_start: 0.8781 (tt0) cc_final: 0.8303 (tt0) REVERT: A 167 CYS cc_start: 0.7872 (m) cc_final: 0.7362 (p) REVERT: A 186 LEU cc_start: 0.8206 (mm) cc_final: 0.7785 (mm) REVERT: A 354 LYS cc_start: 0.8020 (tttm) cc_final: 0.7728 (tttp) REVERT: A 426 ASP cc_start: 0.8236 (t70) cc_final: 0.7856 (t70) REVERT: D 59 ARG cc_start: 0.8956 (mmm-85) cc_final: 0.8645 (mmm-85) REVERT: D 77 ASP cc_start: 0.7299 (m-30) cc_final: 0.6887 (m-30) REVERT: D 114 TRP cc_start: 0.7573 (m-10) cc_final: 0.7047 (m-10) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1561 time to fit residues: 29.8433 Evaluate side-chains 132 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 15 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 146 ASN A 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4123 Z= 0.194 Angle : 0.655 7.270 5595 Z= 0.329 Chirality : 0.044 0.152 650 Planarity : 0.005 0.063 702 Dihedral : 4.402 15.797 570 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.62 % Allowed : 14.58 % Favored : 83.80 % 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: 0.93 (0.37), residues: 524 helix: 1.42 (0.28), residues: 346 sheet: -0.43 (0.80), residues: 50 loop : -1.06 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 328 HIS 0.002 0.001 HIS D 101 PHE 0.014 0.002 PHE A 334 TYR 0.019 0.001 TYR A 182 ARG 0.004 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8250 (mp) cc_final: 0.7816 (mm) REVERT: A 167 CYS cc_start: 0.7709 (m) cc_final: 0.7259 (p) REVERT: A 178 PHE cc_start: 0.7013 (t80) cc_final: 0.6786 (t80) REVERT: A 243 TYR cc_start: 0.8258 (t80) cc_final: 0.8004 (t80) REVERT: A 305 ASN cc_start: 0.8419 (m-40) cc_final: 0.8216 (m110) REVERT: A 354 LYS cc_start: 0.8052 (tttm) cc_final: 0.7730 (tttp) REVERT: A 426 ASP cc_start: 0.8403 (t70) cc_final: 0.7817 (t70) REVERT: A 462 LEU cc_start: 0.8431 (mm) cc_final: 0.8121 (mm) REVERT: D 77 ASP cc_start: 0.7519 (m-30) cc_final: 0.7142 (m-30) REVERT: D 114 TRP cc_start: 0.7423 (m-10) cc_final: 0.6800 (m-10) outliers start: 7 outliers final: 5 residues processed: 144 average time/residue: 0.1705 time to fit residues: 30.0064 Evaluate side-chains 136 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4123 Z= 0.167 Angle : 0.620 7.224 5595 Z= 0.308 Chirality : 0.043 0.166 650 Planarity : 0.005 0.045 702 Dihedral : 4.231 13.920 570 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.08 % Allowed : 18.98 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.37), residues: 524 helix: 1.60 (0.28), residues: 344 sheet: -0.33 (0.80), residues: 50 loop : -1.01 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 318 HIS 0.004 0.001 HIS D 101 PHE 0.015 0.001 PHE A 176 TYR 0.011 0.001 TYR A 422 ARG 0.004 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 0.397 Fit side-chains REVERT: A 22 ILE cc_start: 0.8204 (mp) cc_final: 0.7888 (mm) REVERT: A 127 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 176 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8325 (t80) REVERT: A 178 PHE cc_start: 0.7141 (t80) cc_final: 0.6872 (t80) REVERT: A 186 LEU cc_start: 0.8267 (mm) cc_final: 0.8032 (mm) REVERT: A 354 LYS cc_start: 0.8029 (tttm) cc_final: 0.7695 (tttp) REVERT: A 397 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6886 (ttm) REVERT: A 462 LEU cc_start: 0.8395 (mm) cc_final: 0.8104 (mm) REVERT: D 77 ASP cc_start: 0.7456 (m-30) cc_final: 0.7071 (m-30) REVERT: D 114 TRP cc_start: 0.7576 (m-10) cc_final: 0.6950 (m-10) outliers start: 9 outliers final: 5 residues processed: 151 average time/residue: 0.1542 time to fit residues: 28.8998 Evaluate side-chains 135 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 142 GLN A 146 ASN A 192 GLN A 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4123 Z= 0.213 Angle : 0.647 10.470 5595 Z= 0.320 Chirality : 0.043 0.179 650 Planarity : 0.005 0.042 702 Dihedral : 4.185 13.599 570 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.40 % Allowed : 21.76 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.37), residues: 524 helix: 1.64 (0.28), residues: 343 sheet: -0.27 (0.80), residues: 50 loop : -0.88 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 328 HIS 0.003 0.001 HIS D 101 PHE 0.016 0.002 PHE A 348 TYR 0.019 0.001 TYR A 182 ARG 0.006 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8212 (mp) cc_final: 0.7902 (mm) REVERT: A 127 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 134 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 178 PHE cc_start: 0.7258 (t80) cc_final: 0.7021 (t80) REVERT: A 186 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 305 ASN cc_start: 0.8538 (m-40) cc_final: 0.8311 (m110) REVERT: A 354 LYS cc_start: 0.8037 (tttm) cc_final: 0.7778 (tttp) REVERT: A 413 ARG cc_start: 0.8502 (ptm160) cc_final: 0.8245 (ptm160) REVERT: A 426 ASP cc_start: 0.8519 (t70) cc_final: 0.7840 (t70) REVERT: A 462 LEU cc_start: 0.8343 (mm) cc_final: 0.8032 (mm) REVERT: D 77 ASP cc_start: 0.7530 (m-30) cc_final: 0.7151 (m-30) REVERT: D 114 TRP cc_start: 0.7619 (m-10) cc_final: 0.6959 (m-10) outliers start: 19 outliers final: 10 residues processed: 149 average time/residue: 0.1618 time to fit residues: 30.0778 Evaluate side-chains 148 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4123 Z= 0.173 Angle : 0.635 10.357 5595 Z= 0.309 Chirality : 0.043 0.175 650 Planarity : 0.004 0.035 702 Dihedral : 4.127 14.850 570 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.40 % Allowed : 23.61 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.38), residues: 524 helix: 1.65 (0.28), residues: 343 sheet: -0.23 (0.81), residues: 50 loop : -0.76 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 328 HIS 0.002 0.000 HIS D 101 PHE 0.015 0.001 PHE A 348 TYR 0.017 0.001 TYR A 182 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8119 (mp) cc_final: 0.7836 (mm) REVERT: A 127 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 134 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8104 (mm) REVERT: A 142 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: A 178 PHE cc_start: 0.7223 (t80) cc_final: 0.6960 (t80) REVERT: A 186 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 305 ASN cc_start: 0.8506 (m-40) cc_final: 0.8254 (m110) REVERT: A 354 LYS cc_start: 0.8005 (tttm) cc_final: 0.7742 (tttp) REVERT: A 462 LEU cc_start: 0.8369 (mm) cc_final: 0.8102 (mm) REVERT: D 77 ASP cc_start: 0.7503 (m-30) cc_final: 0.7112 (m-30) REVERT: D 114 TRP cc_start: 0.7619 (m-10) cc_final: 0.6963 (m-10) outliers start: 19 outliers final: 12 residues processed: 159 average time/residue: 0.1453 time to fit residues: 29.0463 Evaluate side-chains 151 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4123 Z= 0.208 Angle : 0.656 10.014 5595 Z= 0.322 Chirality : 0.044 0.180 650 Planarity : 0.004 0.051 702 Dihedral : 4.145 14.825 570 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.24 % Allowed : 25.69 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.37), residues: 524 helix: 1.58 (0.28), residues: 343 sheet: -0.16 (0.82), residues: 50 loop : -0.74 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 328 HIS 0.002 0.001 HIS D 101 PHE 0.016 0.001 PHE A 348 TYR 0.013 0.001 TYR A 182 ARG 0.005 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8209 (mp) cc_final: 0.7941 (mm) REVERT: A 127 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 134 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7917 (mm) REVERT: A 142 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: A 178 PHE cc_start: 0.7292 (t80) cc_final: 0.7040 (t80) REVERT: A 186 LEU cc_start: 0.8347 (mm) cc_final: 0.8121 (mm) REVERT: A 305 ASN cc_start: 0.8507 (m-40) cc_final: 0.8216 (m110) REVERT: A 354 LYS cc_start: 0.8005 (tttm) cc_final: 0.7738 (tttp) REVERT: A 462 LEU cc_start: 0.8360 (mm) cc_final: 0.8089 (mm) REVERT: D 77 ASP cc_start: 0.7527 (m-30) cc_final: 0.7164 (m-30) REVERT: D 114 TRP cc_start: 0.7647 (m-10) cc_final: 0.6971 (m-10) outliers start: 14 outliers final: 12 residues processed: 145 average time/residue: 0.1548 time to fit residues: 28.0580 Evaluate side-chains 148 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4123 Z= 0.194 Angle : 0.654 9.787 5595 Z= 0.319 Chirality : 0.043 0.170 650 Planarity : 0.004 0.035 702 Dihedral : 4.090 14.010 570 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.70 % Allowed : 25.00 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.38), residues: 524 helix: 1.58 (0.28), residues: 343 sheet: -0.11 (0.82), residues: 50 loop : -0.73 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 328 HIS 0.001 0.000 HIS D 101 PHE 0.015 0.001 PHE A 348 TYR 0.016 0.001 TYR A 182 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8157 (mp) cc_final: 0.7897 (mm) REVERT: A 127 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 178 PHE cc_start: 0.7249 (t80) cc_final: 0.7007 (t80) REVERT: A 186 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8051 (mm) REVERT: A 305 ASN cc_start: 0.8475 (m-40) cc_final: 0.8205 (m110) REVERT: A 354 LYS cc_start: 0.7960 (tttm) cc_final: 0.7686 (tttp) REVERT: A 462 LEU cc_start: 0.8351 (mm) cc_final: 0.8093 (mm) REVERT: D 77 ASP cc_start: 0.7467 (m-30) cc_final: 0.7045 (m-30) REVERT: D 114 TRP cc_start: 0.7626 (m-10) cc_final: 0.6949 (m-10) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 0.1509 time to fit residues: 27.8293 Evaluate side-chains 153 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 4123 Z= 0.223 Angle : 0.661 8.862 5595 Z= 0.327 Chirality : 0.045 0.210 650 Planarity : 0.004 0.036 702 Dihedral : 4.098 13.443 570 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.17 % Allowed : 24.54 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.38), residues: 524 helix: 1.62 (0.28), residues: 342 sheet: -0.09 (0.82), residues: 50 loop : -0.64 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 318 HIS 0.001 0.000 HIS D 101 PHE 0.015 0.001 PHE A 348 TYR 0.021 0.001 TYR A 182 ARG 0.003 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7737 (mm-30) REVERT: A 134 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8118 (mm) REVERT: A 178 PHE cc_start: 0.7219 (t80) cc_final: 0.6989 (t80) REVERT: A 186 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8085 (mm) REVERT: A 354 LYS cc_start: 0.7952 (tttm) cc_final: 0.7672 (tttp) REVERT: A 462 LEU cc_start: 0.8396 (mm) cc_final: 0.8139 (mm) REVERT: D 65 ARG cc_start: 0.6941 (ptm160) cc_final: 0.6411 (ptt-90) REVERT: D 77 ASP cc_start: 0.7515 (m-30) cc_final: 0.7120 (m-30) REVERT: D 114 TRP cc_start: 0.7637 (m-10) cc_final: 0.6944 (m-10) outliers start: 18 outliers final: 12 residues processed: 143 average time/residue: 0.1478 time to fit residues: 26.6158 Evaluate side-chains 146 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 30 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 47 optimal weight: 0.2980 chunk 41 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4123 Z= 0.217 Angle : 0.720 11.569 5595 Z= 0.351 Chirality : 0.045 0.197 650 Planarity : 0.005 0.093 702 Dihedral : 4.110 12.860 570 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.94 % Allowed : 24.31 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.38), residues: 524 helix: 1.57 (0.28), residues: 342 sheet: 0.14 (0.83), residues: 49 loop : -0.63 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 318 HIS 0.001 0.000 HIS A 353 PHE 0.015 0.001 PHE A 348 TYR 0.023 0.002 TYR A 243 ARG 0.006 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6335 (tpp-160) cc_final: 0.5485 (ptt180) REVERT: A 22 ILE cc_start: 0.8493 (mm) cc_final: 0.8053 (mm) REVERT: A 127 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 134 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8098 (mm) REVERT: A 186 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 230 MET cc_start: 0.8729 (tmm) cc_final: 0.8510 (tmm) REVERT: A 354 LYS cc_start: 0.7960 (tttm) cc_final: 0.7676 (tttp) REVERT: D 77 ASP cc_start: 0.7494 (m-30) cc_final: 0.7113 (m-30) REVERT: D 114 TRP cc_start: 0.7678 (m-10) cc_final: 0.6951 (m-10) outliers start: 17 outliers final: 11 residues processed: 148 average time/residue: 0.1402 time to fit residues: 26.1461 Evaluate side-chains 148 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4123 Z= 0.222 Angle : 0.709 9.885 5595 Z= 0.346 Chirality : 0.045 0.181 650 Planarity : 0.005 0.096 702 Dihedral : 4.154 16.799 570 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.94 % Allowed : 25.93 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.38), residues: 524 helix: 1.54 (0.28), residues: 342 sheet: 0.18 (0.83), residues: 49 loop : -0.68 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 318 HIS 0.001 0.000 HIS A 353 PHE 0.015 0.001 PHE A 348 TYR 0.027 0.002 TYR A 243 ARG 0.002 0.000 ARG A 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 16 ARG cc_start: 0.5975 (tpp-160) cc_final: 0.4900 (ptt180) REVERT: A 127 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 178 PHE cc_start: 0.7226 (t80) cc_final: 0.7016 (t80) REVERT: A 186 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8137 (mm) REVERT: A 230 MET cc_start: 0.8704 (tmm) cc_final: 0.8504 (tmm) REVERT: A 354 LYS cc_start: 0.7955 (tttm) cc_final: 0.7668 (tttp) REVERT: A 426 ASP cc_start: 0.8439 (t70) cc_final: 0.7779 (t70) REVERT: D 77 ASP cc_start: 0.7486 (m-30) cc_final: 0.7108 (m-30) REVERT: D 114 TRP cc_start: 0.7694 (m-10) cc_final: 0.7025 (m-10) outliers start: 17 outliers final: 14 residues processed: 145 average time/residue: 0.1426 time to fit residues: 26.0442 Evaluate side-chains 152 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.185685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145271 restraints weight = 7096.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.149390 restraints weight = 3935.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.152132 restraints weight = 2599.859| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4123 Z= 0.202 Angle : 0.700 9.394 5595 Z= 0.341 Chirality : 0.044 0.177 650 Planarity : 0.005 0.080 702 Dihedral : 4.079 12.747 570 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.94 % Allowed : 25.93 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.38), residues: 524 helix: 1.61 (0.28), residues: 341 sheet: 0.24 (0.82), residues: 49 loop : -0.70 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 348 TYR 0.025 0.002 TYR A 243 ARG 0.002 0.000 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.70 seconds wall clock time: 23 minutes 51.87 seconds (1431.87 seconds total)