Starting phenix.real_space_refine on Thu Jul 18 21:59:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/07_2024/8wlj_37621.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/07_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_37621/07_2024/8wlj_37621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/07_2024/8wlj_37621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/07_2024/8wlj_37621.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlj_37621/07_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-5388/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: 2.94, per 1000 atoms: 0.73 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: 1.55 Conformation dependent library (CDL) restraints added in 780.3 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: 0.41 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: 1.06 Time building geometry restraints manager: 1.71 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 2.520 nonbonded pdb=" NH1 ARG D 50 " pdb=" O VAL D 51 " model vdw 2.308 2.520 nonbonded pdb=" NH2 ARG A 413 " pdb=" OE2 GLU A 479 " model vdw 2.323 2.520 nonbonded pdb=" O ILE A 301 " pdb=" ND2 ASN A 305 " model vdw 2.337 2.520 nonbonded pdb=" OE2 GLU D 8 " pdb=" N GLY D 117 " model vdw 2.343 2.520 ... (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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- 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 : 0.442 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: 0.1543 time to fit residues: 29.4548 Evaluate side-chains 132 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.0050 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.7474 moved from start: 0.1214 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= 0.192 Angle : 0.649 7.106 5595 Z= 0.325 Chirality : 0.044 0.155 650 Planarity : 0.005 0.077 702 Dihedral : 4.349 15.009 570 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 1.05 (0.37), residues: 524 helix: 1.46 (0.28), residues: 346 sheet: 0.34 (0.86), residues: 42 loop : -1.11 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 328 HIS 0.003 0.001 HIS D 101 PHE 0.014 0.001 PHE A 334 TYR 0.019 0.001 TYR A 182 ARG 0.006 0.000 ARG D 50 *********************** 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 147 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8263 (mp) cc_final: 0.7825 (mm) REVERT: A 138 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8474 (tttp) REVERT: A 167 CYS cc_start: 0.7683 (m) cc_final: 0.7245 (p) REVERT: A 178 PHE cc_start: 0.7133 (t80) cc_final: 0.6906 (t80) REVERT: A 243 TYR cc_start: 0.8254 (t80) cc_final: 0.8041 (t80) REVERT: A 328 TRP cc_start: 0.7888 (p-90) cc_final: 0.7675 (p-90) REVERT: A 354 LYS cc_start: 0.8045 (tttm) cc_final: 0.7728 (tttp) REVERT: A 462 LEU cc_start: 0.8429 (mm) cc_final: 0.8121 (mm) REVERT: D 77 ASP cc_start: 0.7423 (m-30) cc_final: 0.7007 (m-30) REVERT: D 114 TRP cc_start: 0.7539 (m-10) cc_final: 0.6963 (m-10) outliers start: 7 outliers final: 5 residues processed: 142 average time/residue: 0.1615 time to fit residues: 27.9184 Evaluate side-chains 133 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7528 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4123 Z= 0.234 Angle : 0.640 7.484 5595 Z= 0.321 Chirality : 0.044 0.159 650 Planarity : 0.005 0.047 702 Dihedral : 4.289 14.040 570 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.78 % Allowed : 19.91 % Favored : 77.31 % 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: 1.28 (0.37), residues: 524 helix: 1.61 (0.28), residues: 346 sheet: 0.36 (0.87), residues: 42 loop : -0.92 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 318 HIS 0.004 0.001 HIS D 101 PHE 0.017 0.002 PHE A 176 TYR 0.013 0.001 TYR A 422 ARG 0.005 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 150 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8293 (mp) cc_final: 0.7902 (mm) REVERT: A 127 GLU cc_start: 0.8208 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 176 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8384 (t80) REVERT: A 178 PHE cc_start: 0.7242 (t80) cc_final: 0.6973 (t80) REVERT: A 186 LEU cc_start: 0.8299 (mm) cc_final: 0.8041 (mm) REVERT: A 312 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8165 (tp30) REVERT: A 345 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 354 LYS cc_start: 0.8040 (tttm) cc_final: 0.7792 (tttp) REVERT: A 426 ASP cc_start: 0.8462 (t70) cc_final: 0.7989 (t70) REVERT: A 430 CYS cc_start: 0.6993 (t) cc_final: 0.6585 (t) REVERT: A 462 LEU cc_start: 0.8409 (mm) cc_final: 0.8106 (mm) REVERT: D 77 ASP cc_start: 0.7448 (m-30) cc_final: 0.7039 (m-30) outliers start: 12 outliers final: 7 residues processed: 142 average time/residue: 0.1550 time to fit residues: 27.2548 Evaluate side-chains 143 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 397 MET 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: 0.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 192 GLN A 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4123 Z= 0.212 Angle : 0.645 8.063 5595 Z= 0.319 Chirality : 0.043 0.133 650 Planarity : 0.004 0.039 702 Dihedral : 4.213 13.800 570 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.17 % Allowed : 22.92 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.38), residues: 524 helix: 1.67 (0.28), residues: 343 sheet: 0.51 (0.86), residues: 42 loop : -0.88 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 318 HIS 0.003 0.001 HIS D 101 PHE 0.016 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.004 0.000 ARG A 189 *********************** 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 156 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8236 (mp) cc_final: 0.7900 (mm) REVERT: A 127 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 134 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8182 (mm) REVERT: A 142 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: A 176 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8355 (t80) REVERT: A 186 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8049 (mm) REVERT: A 221 MET cc_start: 0.9167 (tpp) cc_final: 0.8843 (tpp) REVERT: A 312 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8206 (tp30) REVERT: A 345 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8414 (p) REVERT: A 354 LYS cc_start: 0.8047 (tttm) cc_final: 0.7789 (tttp) REVERT: A 426 ASP cc_start: 0.8519 (t70) cc_final: 0.7941 (t70) REVERT: A 462 LEU cc_start: 0.8346 (mm) cc_final: 0.8031 (mm) REVERT: D 77 ASP cc_start: 0.7439 (m-30) cc_final: 0.7028 (m-30) REVERT: D 88 ASP cc_start: 0.3512 (OUTLIER) cc_final: 0.3013 (t70) outliers start: 18 outliers final: 9 residues processed: 145 average time/residue: 0.1515 time to fit residues: 27.3779 Evaluate side-chains 147 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 176 PHE 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 287 THR Chi-restraints excluded: chain A residue 345 THR 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 35 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 88 ASP 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: 0.3980 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.0060 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.0570 overall best weight: 0.6716 ------------------------------------------------------------------------------- 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 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4123 Z= 0.189 Angle : 0.634 7.470 5595 Z= 0.311 Chirality : 0.043 0.162 650 Planarity : 0.004 0.035 702 Dihedral : 4.133 13.708 570 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.40 % Allowed : 22.45 % Favored : 73.15 % 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: 1.42 (0.38), residues: 524 helix: 1.71 (0.28), residues: 343 sheet: 0.64 (0.86), residues: 42 loop : -0.87 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 318 HIS 0.002 0.001 HIS D 101 PHE 0.016 0.001 PHE A 348 TYR 0.018 0.001 TYR A 182 ARG 0.003 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 154 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.443 Fit side-chains REVERT: A 22 ILE cc_start: 0.8241 (mp) cc_final: 0.7954 (mm) REVERT: A 127 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 134 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8139 (mm) REVERT: A 176 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8335 (t80) REVERT: A 186 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8040 (mm) REVERT: A 354 LYS cc_start: 0.8011 (tttm) cc_final: 0.7739 (tttp) REVERT: A 426 ASP cc_start: 0.8497 (t70) cc_final: 0.7899 (t70) REVERT: A 462 LEU cc_start: 0.8354 (mm) cc_final: 0.8061 (mm) REVERT: D 77 ASP cc_start: 0.7331 (m-30) cc_final: 0.6888 (m-30) REVERT: D 88 ASP cc_start: 0.3565 (OUTLIER) cc_final: 0.3089 (t70) outliers start: 19 outliers final: 10 residues processed: 143 average time/residue: 0.1503 time to fit residues: 27.0058 Evaluate side-chains 143 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 176 PHE 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 287 THR Chi-restraints excluded: chain A residue 345 THR 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 74 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 A 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4123 Z= 0.190 Angle : 0.627 8.320 5595 Z= 0.308 Chirality : 0.043 0.152 650 Planarity : 0.004 0.034 702 Dihedral : 4.090 13.396 570 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.40 % Allowed : 24.31 % 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: 1.44 (0.38), residues: 524 helix: 1.72 (0.28), residues: 343 sheet: 0.75 (0.86), residues: 42 loop : -0.88 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 318 HIS 0.002 0.001 HIS D 101 PHE 0.016 0.001 PHE A 348 TYR 0.016 0.001 TYR A 182 ARG 0.003 0.000 ARG D 50 *********************** 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 162 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8199 (mp) cc_final: 0.7930 (mm) REVERT: A 127 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 134 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (mm) REVERT: A 186 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8047 (mm) REVERT: A 354 LYS cc_start: 0.8003 (tttm) cc_final: 0.7731 (tttp) REVERT: A 462 LEU cc_start: 0.8353 (mm) cc_final: 0.8086 (mm) REVERT: D 77 ASP cc_start: 0.7379 (m-30) cc_final: 0.6956 (m-30) REVERT: D 88 ASP cc_start: 0.3387 (OUTLIER) cc_final: 0.3022 (t70) outliers start: 19 outliers final: 14 residues processed: 150 average time/residue: 0.1398 time to fit residues: 26.6214 Evaluate side-chains 147 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 427 VAL 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 Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4123 Z= 0.207 Angle : 0.643 7.707 5595 Z= 0.316 Chirality : 0.043 0.165 650 Planarity : 0.004 0.034 702 Dihedral : 4.110 15.839 570 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.63 % Allowed : 25.93 % Favored : 69.44 % 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: 1.41 (0.38), residues: 524 helix: 1.68 (0.28), residues: 343 sheet: 0.72 (0.86), residues: 42 loop : -0.84 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 318 HIS 0.002 0.001 HIS D 101 PHE 0.016 0.001 PHE A 348 TYR 0.020 0.001 TYR A 182 ARG 0.003 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 156 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8202 (mp) cc_final: 0.7931 (mm) REVERT: A 127 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 134 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 142 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: A 186 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A 329 GLN cc_start: 0.8892 (mm110) cc_final: 0.8656 (mm-40) REVERT: A 354 LYS cc_start: 0.7977 (tttm) cc_final: 0.7697 (tttp) REVERT: A 462 LEU cc_start: 0.8373 (mm) cc_final: 0.8112 (mm) REVERT: D 77 ASP cc_start: 0.7357 (m-30) cc_final: 0.6912 (m-30) REVERT: D 88 ASP cc_start: 0.3323 (OUTLIER) cc_final: 0.3001 (t70) outliers start: 20 outliers final: 13 residues processed: 143 average time/residue: 0.1430 time to fit residues: 26.3847 Evaluate side-chains 151 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 427 VAL 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 Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8938 ------------------------------------------------------------------------------- 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 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 4123 Z= 0.245 Angle : 0.669 7.550 5595 Z= 0.330 Chirality : 0.044 0.207 650 Planarity : 0.004 0.034 702 Dihedral : 4.109 13.928 570 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.09 % Allowed : 25.93 % Favored : 68.98 % 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: 1.39 (0.38), residues: 524 helix: 1.65 (0.28), residues: 343 sheet: 0.72 (0.86), residues: 42 loop : -0.79 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.016 0.001 PHE A 348 TYR 0.016 0.001 TYR A 182 ARG 0.005 0.000 ARG A 189 *********************** 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 157 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.416 Fit side-chains REVERT: A 22 ILE cc_start: 0.8222 (mp) cc_final: 0.7952 (mm) REVERT: A 127 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 134 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8037 (mm) REVERT: A 186 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8100 (mm) REVERT: A 354 LYS cc_start: 0.7982 (tttm) cc_final: 0.7698 (tttp) REVERT: A 462 LEU cc_start: 0.8403 (mm) cc_final: 0.8155 (mm) REVERT: D 77 ASP cc_start: 0.7362 (m-30) cc_final: 0.6964 (m-30) REVERT: D 88 ASP cc_start: 0.3313 (OUTLIER) cc_final: 0.2998 (t70) outliers start: 22 outliers final: 11 residues processed: 145 average time/residue: 0.1371 time to fit residues: 25.1557 Evaluate side-chains 147 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 THR Chi-restraints excluded: chain A residue 345 THR 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 Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4123 Z= 0.235 Angle : 0.674 7.421 5595 Z= 0.333 Chirality : 0.044 0.172 650 Planarity : 0.004 0.034 702 Dihedral : 4.140 13.781 570 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.63 % Allowed : 27.55 % Favored : 67.82 % 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: 1.36 (0.38), residues: 524 helix: 1.59 (0.28), residues: 343 sheet: 0.75 (0.87), residues: 42 loop : -0.74 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.016 0.001 PHE A 348 TYR 0.021 0.001 TYR A 182 ARG 0.004 0.000 ARG D 50 *********************** 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 153 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8255 (mp) cc_final: 0.7978 (mm) REVERT: A 127 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 134 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8106 (mm) REVERT: A 186 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8108 (mm) REVERT: A 221 MET cc_start: 0.9127 (tpp) cc_final: 0.8580 (mmt) REVERT: A 354 LYS cc_start: 0.7978 (tttm) cc_final: 0.7695 (tttp) REVERT: A 426 ASP cc_start: 0.8463 (t70) cc_final: 0.7601 (t70) REVERT: D 77 ASP cc_start: 0.7351 (m-30) cc_final: 0.6941 (m-30) REVERT: D 88 ASP cc_start: 0.3252 (OUTLIER) cc_final: 0.2986 (t70) outliers start: 20 outliers final: 12 residues processed: 142 average time/residue: 0.1337 time to fit residues: 24.1862 Evaluate side-chains 144 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 THR Chi-restraints excluded: chain A residue 345 THR 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 Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.0170 chunk 42 optimal weight: 6.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 0.060 4123 Z= 0.203 Angle : 0.681 8.559 5595 Z= 0.331 Chirality : 0.045 0.191 650 Planarity : 0.004 0.034 702 Dihedral : 4.178 14.929 570 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.17 % Allowed : 27.08 % Favored : 68.75 % 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: 1.41 (0.38), residues: 524 helix: 1.66 (0.28), residues: 343 sheet: 0.75 (0.88), residues: 42 loop : -0.79 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.015 0.001 PHE A 348 TYR 0.023 0.001 TYR A 243 ARG 0.004 0.000 ARG A 189 ********************** 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: 18 poor density : 138 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8189 (mp) cc_final: 0.7921 (mm) REVERT: A 127 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 134 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8141 (mm) REVERT: A 186 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8140 (mm) REVERT: A 221 MET cc_start: 0.9099 (tpp) cc_final: 0.8546 (mmt) REVERT: A 354 LYS cc_start: 0.7988 (tttm) cc_final: 0.7704 (tttp) REVERT: D 77 ASP cc_start: 0.7339 (m-30) cc_final: 0.6989 (m-30) REVERT: D 114 TRP cc_start: 0.7636 (m-10) cc_final: 0.7286 (m-10) outliers start: 18 outliers final: 13 residues processed: 144 average time/residue: 0.1412 time to fit residues: 25.5442 Evaluate side-chains 145 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 192 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 345 THR 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 5 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.185007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143520 restraints weight = 6973.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147692 restraints weight = 3837.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150384 restraints weight = 2522.085| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4123 Z= 0.211 Angle : 0.688 8.235 5595 Z= 0.336 Chirality : 0.044 0.168 650 Planarity : 0.004 0.034 702 Dihedral : 4.158 13.263 570 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.47 % Allowed : 27.78 % Favored : 68.75 % 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: 1.34 (0.38), residues: 524 helix: 1.60 (0.28), residues: 343 sheet: 0.78 (0.87), residues: 42 loop : -0.82 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 328 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 0.004 0.000 ARG D 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.29 seconds wall clock time: 23 minutes 32.42 seconds (1412.42 seconds total)