Starting phenix.real_space_refine on Fri Nov 15 00:48:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4x_41903/11_2024/8u4x_41903.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4x_41903/11_2024/8u4x_41903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4x_41903/11_2024/8u4x_41903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4x_41903/11_2024/8u4x_41903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4x_41903/11_2024/8u4x_41903.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4x_41903/11_2024/8u4x_41903.cif" } resolution = 2.81 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= 0.020 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 46 5.16 5 C 4963 2.51 5 N 1373 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7873 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3890 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 8.11, per 1000 atoms: 1.03 Number of scatterers: 7873 At special positions: 0 Unit cell: (100.521, 80.811, 102.492, 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 46 16.00 O 1491 8.00 N 1373 7.00 C 4963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 379 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 43.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 18 Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.983A pdb=" N ARG A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 133' Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.820A pdb=" N ARG A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 340 removed outlier: 4.301A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.595A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.951A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 396 " --> pdb=" O MET A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.901A pdb=" N VAL A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.604A pdb=" N GLU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 414 " --> pdb=" O PRO A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 488 through 516 Processing helix chain 'B' and resid 12 through 18 Processing helix chain 'B' and resid 49 through 52 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.984A pdb=" N ARG B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 133' Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.821A pdb=" N ARG B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 340 removed outlier: 4.302A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.595A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.951A pdb=" N ALA B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY B 395 " --> pdb=" O TRP B 391 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.901A pdb=" N VAL B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.605A pdb=" N GLU B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 414 " --> pdb=" O PRO B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 488 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.204A pdb=" N ILE A 43 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS A 37 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU A 33 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A 101 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.580A pdb=" N GLY A 180 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 185 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 169 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN A 275 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 281 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 269 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 449 removed outlier: 3.956A pdb=" N GLN A 444 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.204A pdb=" N ILE B 43 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS B 37 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 33 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU B 101 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.580A pdb=" N GLY B 180 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 171 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU B 185 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 169 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN B 275 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 269 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 377 Processing sheet with id=AA8, first strand: chain 'B' and resid 444 through 449 removed outlier: 3.957A pdb=" N GLN B 444 " --> pdb=" O MET B 480 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1182 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: 2.37 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1456 1.33 - 1.45: 1933 1.45 - 1.57: 4569 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8036 Sorted by residual: bond pdb=" C PRO B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.83e+00 bond pdb=" C PRO A 410 " pdb=" N PRO A 411 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.81e+00 bond pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.57e-01 bond pdb=" CD GLU A 98 " pdb=" OE1 GLU A 98 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.46e-01 ... (remaining 8031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 10457 1.11 - 2.22: 313 2.22 - 3.33: 129 3.33 - 4.44: 14 4.44 - 5.55: 14 Bond angle restraints: 10927 Sorted by residual: angle pdb=" CA GLU A 98 " pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " ideal model delta sigma weight residual 114.10 119.65 -5.55 2.00e+00 2.50e-01 7.70e+00 angle pdb=" CA GLU B 98 " pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.68e+00 angle pdb=" CA GLN B 372 " pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " ideal model delta sigma weight residual 114.10 119.23 -5.13 2.00e+00 2.50e-01 6.59e+00 angle pdb=" CA GLN A 372 " pdb=" CB GLN A 372 " pdb=" CG GLN A 372 " ideal model delta sigma weight residual 114.10 119.18 -5.08 2.00e+00 2.50e-01 6.45e+00 angle pdb=" C PRO B 410 " pdb=" N PRO B 411 " pdb=" CA PRO B 411 " ideal model delta sigma weight residual 120.83 118.40 2.43 1.02e+00 9.61e-01 5.67e+00 ... (remaining 10922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 4016 14.64 - 29.29: 541 29.29 - 43.93: 215 43.93 - 58.58: 77 58.58 - 73.22: 37 Dihedral angle restraints: 4886 sinusoidal: 1994 harmonic: 2892 Sorted by residual: dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 379 " pdb=" CB CYS A 379 " ideal model delta sinusoidal sigma weight residual -86.00 -58.35 -27.65 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CG ARG B 173 " pdb=" CD ARG B 173 " pdb=" NE ARG B 173 " pdb=" CZ ARG B 173 " ideal model delta sinusoidal sigma weight residual 90.00 133.34 -43.34 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG A 173 " pdb=" CD ARG A 173 " pdb=" NE ARG A 173 " pdb=" CZ ARG A 173 " ideal model delta sinusoidal sigma weight residual 90.00 133.32 -43.32 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 4883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 822 0.032 - 0.064: 249 0.064 - 0.095: 83 0.095 - 0.127: 57 0.127 - 0.159: 11 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CB THR A 390 " pdb=" CA THR A 390 " pdb=" OG1 THR A 390 " pdb=" CG2 THR A 390 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB THR B 390 " pdb=" CA THR B 390 " pdb=" OG1 THR B 390 " pdb=" CG2 THR B 390 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA VAL A 97 " pdb=" N VAL A 97 " pdb=" C VAL A 97 " pdb=" CB VAL A 97 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1219 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 409 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 410 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 410 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 410 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 409 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 410 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 410 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 410 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 454 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C LYS A 454 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS A 454 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO A 455 " -0.007 2.00e-02 2.50e+03 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 2 2.05 - 2.76: 1111 2.76 - 3.47: 10709 3.47 - 4.19: 18598 4.19 - 4.90: 32983 Nonbonded interactions: 63403 Sorted by model distance: nonbonded pdb=" C VAL B 11 " pdb=" N LEU B 12 " model vdw 1.334 3.350 nonbonded pdb=" SG CYS B 375 " pdb=" SG CYS B 379 " model vdw 2.032 3.760 nonbonded pdb=" O VAL B 11 " pdb=" N LEU B 12 " model vdw 2.256 3.120 nonbonded pdb=" O GLN B 416 " pdb=" OG SER B 420 " model vdw 2.259 3.040 nonbonded pdb=" O GLN A 416 " pdb=" OG SER A 420 " model vdw 2.259 3.040 ... (remaining 63398 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 12 through 516 or resid 900)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.070 Find NCS groups from input model: 0.300 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.002 0.032 8036 Z= 0.146 Angle : 0.559 5.548 10927 Z= 0.300 Chirality : 0.042 0.159 1222 Planarity : 0.004 0.032 1428 Dihedral : 17.694 73.223 3009 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.11 % Allowed : 27.43 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.85 (0.28), residues: 991 helix: 1.98 (0.27), residues: 370 sheet: -0.28 (0.37), residues: 194 loop : -0.21 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.003 0.001 HIS A 287 PHE 0.008 0.001 PHE B 493 TYR 0.008 0.001 TYR A 172 ARG 0.007 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.895 Fit side-chains REVERT: A 132 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7513 (mtt180) REVERT: A 265 VAL cc_start: 0.8133 (m) cc_final: 0.7904 (p) REVERT: B 40 GLU cc_start: 0.6098 (tt0) cc_final: 0.5838 (tt0) REVERT: B 50 VAL cc_start: 0.7879 (m) cc_final: 0.7583 (t) REVERT: B 118 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7445 (mt-10) REVERT: B 138 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.7157 (mtp180) REVERT: B 206 GLU cc_start: 0.7324 (tp30) cc_final: 0.7042 (tp30) REVERT: B 231 VAL cc_start: 0.7883 (p) cc_final: 0.7621 (m) REVERT: B 265 VAL cc_start: 0.7980 (m) cc_final: 0.7731 (p) REVERT: B 454 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8024 (ttpp) outliers start: 18 outliers final: 10 residues processed: 253 average time/residue: 1.3855 time to fit residues: 367.9292 Evaluate side-chains 234 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 456 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.0370 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 374 HIS A 444 GLN A 468 GLN B 306 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8036 Z= 0.259 Angle : 0.552 5.046 10927 Z= 0.283 Chirality : 0.044 0.136 1222 Planarity : 0.005 0.033 1428 Dihedral : 6.383 53.395 1132 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.98 % Allowed : 21.69 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.72 (0.27), residues: 990 helix: 1.99 (0.26), residues: 379 sheet: -0.38 (0.36), residues: 202 loop : -0.45 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.025 0.002 PHE B 493 TYR 0.010 0.001 TYR A 172 ARG 0.005 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7991 (tp30) cc_final: 0.7715 (mm-30) REVERT: A 504 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 50 VAL cc_start: 0.7998 (m) cc_final: 0.7761 (t) REVERT: B 118 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 163 MET cc_start: 0.8595 (ptm) cc_final: 0.8291 (ptp) REVERT: B 187 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 206 GLU cc_start: 0.7313 (tp30) cc_final: 0.7034 (tp30) REVERT: B 265 VAL cc_start: 0.8324 (m) cc_final: 0.8105 (p) REVERT: B 336 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7524 (mm110) REVERT: B 372 GLN cc_start: 0.7154 (mm110) cc_final: 0.6870 (mp10) REVERT: B 454 LYS cc_start: 0.8363 (ttmm) cc_final: 0.8154 (ttpp) outliers start: 51 outliers final: 19 residues processed: 262 average time/residue: 1.4186 time to fit residues: 390.3835 Evaluate side-chains 239 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 374 HIS A 444 GLN A 468 GLN B 241 GLN B 332 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8036 Z= 0.273 Angle : 0.553 5.241 10927 Z= 0.281 Chirality : 0.043 0.133 1222 Planarity : 0.005 0.035 1428 Dihedral : 6.236 52.832 1123 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.81 % Allowed : 23.33 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.67 (0.27), residues: 990 helix: 1.93 (0.26), residues: 380 sheet: -0.43 (0.36), residues: 200 loop : -0.45 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.035 0.002 PHE B 493 TYR 0.010 0.001 TYR A 172 ARG 0.004 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.836 Fit side-chains REVERT: A 185 GLU cc_start: 0.8144 (tp30) cc_final: 0.7848 (mm-30) REVERT: A 207 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6977 (pt0) REVERT: A 288 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8244 (mtm180) REVERT: A 454 LYS cc_start: 0.8250 (ttmm) cc_final: 0.8006 (ttmm) REVERT: B 50 VAL cc_start: 0.8010 (m) cc_final: 0.7792 (t) REVERT: B 118 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7728 (mt-10) REVERT: B 163 MET cc_start: 0.8622 (ptm) cc_final: 0.8260 (ptp) REVERT: B 187 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7975 (t) REVERT: B 206 GLU cc_start: 0.7307 (tp30) cc_final: 0.7029 (tp30) REVERT: B 235 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: B 336 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7492 (mm110) outliers start: 41 outliers final: 21 residues processed: 254 average time/residue: 1.4060 time to fit residues: 374.4675 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 0.0040 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.0770 chunk 47 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 306 GLN A 374 HIS A 444 GLN A 468 GLN A 510 GLN B 60 GLN B 241 GLN B 306 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8036 Z= 0.192 Angle : 0.522 4.846 10927 Z= 0.266 Chirality : 0.042 0.131 1222 Planarity : 0.004 0.034 1428 Dihedral : 6.095 52.714 1121 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.39 % Allowed : 23.33 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.78 (0.27), residues: 990 helix: 2.10 (0.26), residues: 375 sheet: -0.41 (0.36), residues: 197 loop : -0.42 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.040 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.003 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.853 Fit side-chains REVERT: A 118 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 207 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: A 231 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7568 (p) REVERT: B 50 VAL cc_start: 0.8063 (m) cc_final: 0.7838 (t) REVERT: B 118 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 163 MET cc_start: 0.8583 (ptm) cc_final: 0.8224 (ptp) REVERT: B 187 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7959 (t) REVERT: B 206 GLU cc_start: 0.7295 (tp30) cc_final: 0.7062 (tp30) REVERT: B 235 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6456 (mtm180) REVERT: B 336 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7497 (mm110) outliers start: 46 outliers final: 20 residues processed: 256 average time/residue: 1.3824 time to fit residues: 371.3943 Evaluate side-chains 241 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 374 HIS A 444 GLN A 468 GLN B 60 GLN B 120 GLN B 241 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8036 Z= 0.221 Angle : 0.541 5.057 10927 Z= 0.275 Chirality : 0.043 0.139 1222 Planarity : 0.005 0.035 1428 Dihedral : 6.080 52.505 1121 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.69 % Allowed : 24.50 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.78 (0.27), residues: 990 helix: 2.08 (0.26), residues: 375 sheet: -0.42 (0.36), residues: 200 loop : -0.40 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.045 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8138 (tp30) cc_final: 0.7778 (mm-30) REVERT: A 207 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: A 231 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7562 (p) REVERT: A 384 ASP cc_start: 0.7168 (m-30) cc_final: 0.6949 (m-30) REVERT: B 50 VAL cc_start: 0.8095 (m) cc_final: 0.7883 (t) REVERT: B 118 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7726 (mt-10) REVERT: B 187 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7982 (t) REVERT: B 206 GLU cc_start: 0.7304 (tp30) cc_final: 0.7077 (tp30) REVERT: B 235 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6425 (mtm180) REVERT: B 336 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7488 (mm110) REVERT: B 372 GLN cc_start: 0.7232 (mp10) cc_final: 0.6875 (mp10) REVERT: B 446 VAL cc_start: 0.7823 (t) cc_final: 0.7549 (m) outliers start: 40 outliers final: 26 residues processed: 246 average time/residue: 1.3985 time to fit residues: 361.3607 Evaluate side-chains 245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.0370 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 374 HIS A 444 GLN A 468 GLN B 60 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8036 Z= 0.204 Angle : 0.539 6.467 10927 Z= 0.275 Chirality : 0.042 0.144 1222 Planarity : 0.005 0.047 1428 Dihedral : 6.058 52.499 1121 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.57 % Allowed : 24.62 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.77 (0.27), residues: 990 helix: 2.07 (0.26), residues: 375 sheet: -0.41 (0.36), residues: 197 loop : -0.39 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.045 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 207 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6943 (pt0) REVERT: A 231 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7543 (p) REVERT: A 288 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8160 (mtm180) REVERT: A 336 GLN cc_start: 0.7877 (mm110) cc_final: 0.7544 (mm110) REVERT: B 50 VAL cc_start: 0.8096 (m) cc_final: 0.7880 (t) REVERT: B 118 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 187 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7973 (t) REVERT: B 206 GLU cc_start: 0.7306 (tp30) cc_final: 0.7081 (tp30) REVERT: B 235 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6445 (mtm180) REVERT: B 336 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7472 (mm110) outliers start: 39 outliers final: 21 residues processed: 245 average time/residue: 1.4357 time to fit residues: 369.1111 Evaluate side-chains 238 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 295 HIS B 444 GLN B 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8036 Z= 0.304 Angle : 0.593 6.053 10927 Z= 0.302 Chirality : 0.045 0.153 1222 Planarity : 0.005 0.045 1428 Dihedral : 6.228 52.120 1121 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.57 % Allowed : 25.21 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.62 (0.27), residues: 990 helix: 1.89 (0.26), residues: 375 sheet: -0.45 (0.36), residues: 200 loop : -0.47 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.023 0.002 PHE B 493 TYR 0.010 0.001 TYR A 172 ARG 0.009 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.879 Fit side-chains REVERT: A 118 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 185 GLU cc_start: 0.8215 (tp30) cc_final: 0.7839 (mm-30) REVERT: A 207 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6990 (pt0) REVERT: A 231 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7621 (p) REVERT: A 336 GLN cc_start: 0.7898 (mm110) cc_final: 0.7585 (mm110) REVERT: A 443 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7790 (mmtm) REVERT: B 50 VAL cc_start: 0.8065 (m) cc_final: 0.7855 (t) REVERT: B 76 GLU cc_start: 0.8197 (tp30) cc_final: 0.7962 (mm-30) REVERT: B 187 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8032 (t) REVERT: B 235 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6424 (mtm180) REVERT: B 336 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7483 (mm110) outliers start: 39 outliers final: 23 residues processed: 248 average time/residue: 1.4344 time to fit residues: 373.6113 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 47 optimal weight: 0.0040 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 306 GLN B 468 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8036 Z= 0.250 Angle : 0.595 7.904 10927 Z= 0.301 Chirality : 0.043 0.160 1222 Planarity : 0.005 0.057 1428 Dihedral : 6.197 52.161 1121 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.10 % Allowed : 26.26 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.63 (0.27), residues: 990 helix: 1.92 (0.26), residues: 375 sheet: -0.47 (0.36), residues: 198 loop : -0.46 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.025 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.008 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.769 Fit side-chains REVERT: A 118 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 185 GLU cc_start: 0.8205 (tp30) cc_final: 0.7842 (mm-30) REVERT: A 207 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6930 (pt0) REVERT: A 231 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 288 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8162 (mtm180) REVERT: A 336 GLN cc_start: 0.7897 (mm110) cc_final: 0.7571 (mm110) REVERT: A 372 GLN cc_start: 0.7252 (mp10) cc_final: 0.6917 (mp10) REVERT: A 480 MET cc_start: 0.8134 (mmm) cc_final: 0.7770 (mmm) REVERT: B 50 VAL cc_start: 0.8081 (m) cc_final: 0.7870 (t) REVERT: B 76 GLU cc_start: 0.8194 (tp30) cc_final: 0.7951 (mm-30) REVERT: B 105 LEU cc_start: 0.8471 (mm) cc_final: 0.8218 (mp) REVERT: B 187 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.8045 (t) REVERT: B 235 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6437 (mtm180) REVERT: B 336 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7450 (mm110) outliers start: 35 outliers final: 23 residues processed: 245 average time/residue: 1.4180 time to fit residues: 364.2885 Evaluate side-chains 245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 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 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 444 GLN B 468 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8036 Z= 0.300 Angle : 0.614 7.627 10927 Z= 0.311 Chirality : 0.044 0.162 1222 Planarity : 0.005 0.059 1428 Dihedral : 6.260 52.147 1121 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.99 % Allowed : 26.73 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.55 (0.27), residues: 990 helix: 1.87 (0.26), residues: 375 sheet: -0.51 (0.36), residues: 198 loop : -0.52 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.013 0.002 PHE A 34 TYR 0.009 0.001 TYR A 172 ARG 0.008 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.907 Fit side-chains REVERT: A 185 GLU cc_start: 0.8230 (tp30) cc_final: 0.7879 (mm-30) REVERT: A 207 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: A 231 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7616 (p) REVERT: A 288 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8156 (mtm180) REVERT: A 336 GLN cc_start: 0.7897 (mm110) cc_final: 0.7576 (mm110) REVERT: A 480 MET cc_start: 0.8129 (mmm) cc_final: 0.7758 (mmm) REVERT: B 50 VAL cc_start: 0.8078 (m) cc_final: 0.7874 (t) REVERT: B 76 GLU cc_start: 0.8208 (tp30) cc_final: 0.7958 (mm-30) REVERT: B 187 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.8007 (t) REVERT: B 235 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6420 (mtm180) REVERT: B 336 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7463 (mm110) outliers start: 34 outliers final: 28 residues processed: 242 average time/residue: 1.4356 time to fit residues: 364.1420 Evaluate side-chains 247 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 60 GLN B 144 HIS B 468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8036 Z= 0.270 Angle : 0.616 7.589 10927 Z= 0.312 Chirality : 0.044 0.183 1222 Planarity : 0.005 0.063 1428 Dihedral : 6.259 52.048 1121 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.99 % Allowed : 26.49 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.54 (0.27), residues: 990 helix: 1.88 (0.26), residues: 375 sheet: -0.53 (0.36), residues: 198 loop : -0.54 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.012 0.002 PHE A 34 TYR 0.009 0.001 TYR A 172 ARG 0.008 0.001 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.969 Fit side-chains REVERT: A 185 GLU cc_start: 0.8214 (tp30) cc_final: 0.7865 (mm-30) REVERT: A 207 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6956 (pt0) REVERT: A 231 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7615 (p) REVERT: A 288 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8159 (mtm180) REVERT: A 372 GLN cc_start: 0.7278 (mp10) cc_final: 0.6911 (mp10) REVERT: A 480 MET cc_start: 0.8144 (mmm) cc_final: 0.7771 (mmm) REVERT: B 50 VAL cc_start: 0.8082 (m) cc_final: 0.7881 (t) REVERT: B 76 GLU cc_start: 0.8207 (tp30) cc_final: 0.7961 (mm-30) REVERT: B 105 LEU cc_start: 0.8492 (mm) cc_final: 0.8228 (mp) REVERT: B 187 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.8023 (t) REVERT: B 235 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6410 (mtm180) REVERT: B 288 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8113 (mtt90) REVERT: B 336 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7459 (mm110) outliers start: 34 outliers final: 27 residues processed: 242 average time/residue: 1.4500 time to fit residues: 367.9858 Evaluate side-chains 245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 336 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 60 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.139114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126114 restraints weight = 10448.267| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.89 r_work: 0.3592 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8036 Z= 0.293 Angle : 0.632 7.516 10927 Z= 0.321 Chirality : 0.045 0.186 1222 Planarity : 0.005 0.064 1428 Dihedral : 6.307 52.236 1121 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.99 % Allowed : 26.85 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.51 (0.27), residues: 990 helix: 1.84 (0.26), residues: 375 sheet: -0.56 (0.36), residues: 198 loop : -0.54 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.013 0.002 PHE A 34 TYR 0.009 0.001 TYR A 172 ARG 0.008 0.001 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5377.25 seconds wall clock time: 95 minutes 46.34 seconds (5746.34 seconds total)