Starting phenix.real_space_refine on Tue Jan 14 17:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izu_61042/01_2025/9izu_61042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izu_61042/01_2025/9izu_61042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izu_61042/01_2025/9izu_61042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izu_61042/01_2025/9izu_61042.map" model { file = "/net/cci-nas-00/data/ceres_data/9izu_61042/01_2025/9izu_61042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izu_61042/01_2025/9izu_61042.cif" } resolution = 3.7 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= 0.024 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 47 5.16 5 C 4513 2.51 5 N 1224 2.21 5 O 1321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7105 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3581 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 26, 'TRANS': 443} Chain breaks: 1 Chain: "D" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3524 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 25, 'TRANS': 437} Chain breaks: 2 Time building chain proxies: 4.96, per 1000 atoms: 0.70 Number of scatterers: 7105 At special positions: 0 Unit cell: (62.624, 83.224, 117.008, 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 47 16.00 O 1321 8.00 N 1224 7.00 C 4513 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 48.6% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'C' and resid 43 through 64 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 65 through 83 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 98 through 118 removed outlier: 3.690A pdb=" N SER C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.569A pdb=" N MET C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 170 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.694A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 Processing helix chain 'C' and resid 265 through 278 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 296 through 310 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 328 through 345 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'D' and resid 43 through 64 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 98 through 119 removed outlier: 3.575A pdb=" N VAL D 119 " --> pdb=" O HIS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.082A pdb=" N MET D 123 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 170 Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.685A pdb=" N THR D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.677A pdb=" N HIS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 278 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 296 through 299 Processing helix chain 'D' and resid 300 through 311 removed outlier: 3.536A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 345 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 398 through 409 removed outlier: 3.567A pdb=" N ASN D 409 " --> pdb=" O ILE D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 467 through 475 Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 28 Processing sheet with id=AA2, first strand: chain 'C' and resid 127 through 132 removed outlier: 8.413A pdb=" N MET C 128 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N SER C 139 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 130 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU C 137 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL D 437 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR C 479 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL D 439 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 481 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 415 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS D 257 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY D 258 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL D 294 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 260 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 396 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU D 391 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR D 370 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL D 393 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 372 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLU D 395 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY D 353 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR D 370 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU D 351 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 372 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 349 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 203 through 205 removed outlier: 7.505A pdb=" N VAL C 146 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 225 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 148 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE C 227 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 150 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 251 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 349 through 351 removed outlier: 5.853A pdb=" N ILE C 349 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER C 373 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 351 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU C 395 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C 258 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 294 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 260 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 415 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 437 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 24 through 28 removed outlier: 3.651A pdb=" N GLY D 37 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.888A pdb=" N VAL D 146 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 224 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 228 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS D 223 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN D 249 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE D 225 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ASN D 251 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE D 227 " --> pdb=" O ASN D 251 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1020 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: 2.15 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2351 1.34 - 1.46: 1390 1.46 - 1.58: 3425 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 7244 Sorted by residual: bond pdb=" N SER D 3 " pdb=" CA SER D 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N SER C 3 " pdb=" CA SER C 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" CA GLY D 438 " pdb=" C GLY D 438 " ideal model delta sigma weight residual 1.516 1.525 -0.010 8.10e-03 1.52e+04 1.44e+00 bond pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta sigma weight residual 1.458 1.472 -0.014 1.30e-02 5.92e+03 1.24e+00 bond pdb=" N SER C 30 " pdb=" CA SER C 30 " ideal model delta sigma weight residual 1.458 1.471 -0.014 1.33e-02 5.65e+03 1.09e+00 ... (remaining 7239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 9590 1.14 - 2.29: 162 2.29 - 3.43: 43 3.43 - 4.57: 17 4.57 - 5.71: 1 Bond angle restraints: 9813 Sorted by residual: angle pdb=" C ILE D 159 " pdb=" CA ILE D 159 " pdb=" CB ILE D 159 " ideal model delta sigma weight residual 113.70 110.79 2.91 9.50e-01 1.11e+00 9.37e+00 angle pdb=" N VAL C 119 " pdb=" CA VAL C 119 " pdb=" C VAL C 119 " ideal model delta sigma weight residual 112.29 109.63 2.66 9.40e-01 1.13e+00 8.01e+00 angle pdb=" N ILE D 36 " pdb=" CA ILE D 36 " pdb=" C ILE D 36 " ideal model delta sigma weight residual 113.20 110.55 2.65 9.60e-01 1.09e+00 7.63e+00 angle pdb=" CA ASN C 29 " pdb=" C ASN C 29 " pdb=" N SER C 30 " ideal model delta sigma weight residual 116.21 119.58 -3.37 1.33e+00 5.65e-01 6.43e+00 angle pdb=" N ILE D 159 " pdb=" CA ILE D 159 " pdb=" C ILE D 159 " ideal model delta sigma weight residual 112.67 109.58 3.09 1.25e+00 6.40e-01 6.12e+00 ... (remaining 9808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 4253 16.01 - 32.02: 103 32.02 - 48.02: 20 48.02 - 64.03: 5 64.03 - 80.04: 1 Dihedral angle restraints: 4382 sinusoidal: 1732 harmonic: 2650 Sorted by residual: dihedral pdb=" CA ARG C 334 " pdb=" CB ARG C 334 " pdb=" CG ARG C 334 " pdb=" CD ARG C 334 " ideal model delta sinusoidal sigma weight residual -180.00 -122.99 -57.01 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA LYS D 468 " pdb=" CB LYS D 468 " pdb=" CG LYS D 468 " pdb=" CD LYS D 468 " ideal model delta sinusoidal sigma weight residual 60.00 103.43 -43.43 3 1.50e+01 4.44e-03 7.81e+00 dihedral pdb=" N TRP D 484 " pdb=" CA TRP D 484 " pdb=" CB TRP D 484 " pdb=" CG TRP D 484 " ideal model delta sinusoidal sigma weight residual -180.00 -136.88 -43.12 3 1.50e+01 4.44e-03 7.75e+00 ... (remaining 4379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 718 0.025 - 0.051: 208 0.051 - 0.076: 69 0.076 - 0.101: 60 0.101 - 0.127: 61 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CA VAL D 39 " pdb=" N VAL D 39 " pdb=" C VAL D 39 " pdb=" CB VAL D 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE C 225 " pdb=" N ILE C 225 " pdb=" C ILE C 225 " pdb=" CB ILE C 225 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL C 39 " pdb=" N VAL C 39 " pdb=" C VAL C 39 " pdb=" CB VAL C 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1113 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 151 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO D 152 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO C 302 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 39 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO D 40 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 40 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 40 " -0.015 5.00e-02 4.00e+02 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 95 2.66 - 3.22: 7149 3.22 - 3.78: 11250 3.78 - 4.34: 15357 4.34 - 4.90: 25285 Nonbonded interactions: 59136 Sorted by model distance: nonbonded pdb=" O LEU D 193 " pdb=" OG SER D 196 " model vdw 2.095 3.040 nonbonded pdb=" OG SER D 348 " pdb=" OD1 ASN D 374 " model vdw 2.163 3.040 nonbonded pdb=" NZ LYS D 255 " pdb=" O TYR D 382 " model vdw 2.173 3.120 nonbonded pdb=" ND2 ASN D 33 " pdb=" O ASN D 363 " model vdw 2.218 3.120 nonbonded pdb=" OD1 ASP D 340 " pdb=" NH1 ARG D 354 " model vdw 2.238 3.120 ... (remaining 59131 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 'C' and (resid 3 through 125 or resid 134 through 450 or resid 466 throug \ h 486)) selection = (chain 'D' and (resid 3 through 450 or resid 466 through 486)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.040 Process input model: 20.110 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1532 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 7244 Z= 0.128 Angle : 0.447 5.714 9813 Z= 0.258 Chirality : 0.041 0.127 1116 Planarity : 0.002 0.031 1274 Dihedral : 7.952 80.041 2680 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 923 helix: 1.13 (0.25), residues: 402 sheet: -0.82 (0.35), residues: 173 loop : -1.75 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 484 HIS 0.002 0.000 HIS C 244 PHE 0.013 0.001 PHE C 164 TYR 0.006 0.001 TYR C 411 ARG 0.002 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: -0.1731 (mtt) cc_final: -0.2548 (mtt) REVERT: D 54 CYS cc_start: 0.4254 (m) cc_final: 0.3872 (m) REVERT: D 259 VAL cc_start: 0.6866 (t) cc_final: 0.6664 (t) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2451 time to fit residues: 40.7992 Evaluate side-chains 76 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 115 HIS C 207 HIS C 318 GLN C 365 ASN C 421 ASN ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 365 ASN D 378 ASN D 483 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5563 r_free = 0.5563 target = 0.249230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5459 r_free = 0.5459 target = 0.216948 restraints weight = 21200.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.5459 r_free = 0.5459 target = 0.216935 restraints weight = 23132.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5459 r_free = 0.5459 target = 0.216932 restraints weight = 23141.022| |-----------------------------------------------------------------------------| r_work (final): 0.5370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4082 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7244 Z= 0.295 Angle : 0.734 7.342 9813 Z= 0.383 Chirality : 0.049 0.200 1116 Planarity : 0.006 0.065 1274 Dihedral : 4.371 17.431 978 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.01 % Allowed : 7.32 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 923 helix: 1.31 (0.25), residues: 415 sheet: -0.57 (0.37), residues: 177 loop : -1.43 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 162 HIS 0.011 0.001 HIS C 115 PHE 0.028 0.003 PHE C 164 TYR 0.029 0.002 TYR D 428 ARG 0.012 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6191 (mpp) cc_final: 0.5372 (mpp) REVERT: C 306 GLU cc_start: 0.9157 (pt0) cc_final: 0.8918 (tm-30) REVERT: C 449 MET cc_start: 0.8254 (mtp) cc_final: 0.7798 (mmm) REVERT: D 28 HIS cc_start: 0.4031 (OUTLIER) cc_final: 0.3793 (p-80) REVERT: D 168 MET cc_start: 0.5414 (OUTLIER) cc_final: 0.3105 (mtt) REVERT: D 259 VAL cc_start: 0.9173 (t) cc_final: 0.8815 (p) REVERT: D 479 THR cc_start: 0.3244 (OUTLIER) cc_final: 0.2946 (t) outliers start: 23 outliers final: 9 residues processed: 103 average time/residue: 0.2304 time to fit residues: 30.9391 Evaluate side-chains 82 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C 374 ASN C 421 ASN C 440 ASN C 483 GLN ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5553 r_free = 0.5553 target = 0.248108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.225694 restraints weight = 36585.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.226575 restraints weight = 32346.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.226575 restraints weight = 29971.083| |-----------------------------------------------------------------------------| r_work (final): 0.5234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4252 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7244 Z= 0.268 Angle : 0.668 11.162 9813 Z= 0.340 Chirality : 0.047 0.282 1116 Planarity : 0.005 0.053 1274 Dihedral : 4.554 22.917 978 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.09 % Allowed : 10.20 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 923 helix: 1.32 (0.25), residues: 417 sheet: -0.35 (0.39), residues: 167 loop : -1.55 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 61 HIS 0.006 0.001 HIS D 219 PHE 0.018 0.002 PHE C 174 TYR 0.014 0.002 TYR D 428 ARG 0.005 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6180 (mpp) cc_final: 0.5510 (mpp) REVERT: C 306 GLU cc_start: 0.9118 (pt0) cc_final: 0.8799 (tm-30) REVERT: C 449 MET cc_start: 0.8070 (mtp) cc_final: 0.7590 (mmm) REVERT: D 163 MET cc_start: 0.6146 (ptp) cc_final: 0.5924 (ptp) REVERT: D 168 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.2828 (mtt) REVERT: D 259 VAL cc_start: 0.8990 (t) cc_final: 0.8614 (p) REVERT: D 379 MET cc_start: 0.5632 (ptm) cc_final: 0.4873 (ppp) outliers start: 16 outliers final: 12 residues processed: 87 average time/residue: 0.2135 time to fit residues: 24.9257 Evaluate side-chains 81 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 ASN D 210 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 ASN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5459 r_free = 0.5459 target = 0.228752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5386 r_free = 0.5386 target = 0.190587 restraints weight = 20690.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.187648 restraints weight = 22260.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.5318 r_free = 0.5318 target = 0.187426 restraints weight = 25265.884| |-----------------------------------------------------------------------------| r_work (final): 0.5019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 7244 Z= 0.352 Angle : 0.743 10.405 9813 Z= 0.386 Chirality : 0.050 0.320 1116 Planarity : 0.006 0.055 1274 Dihedral : 5.173 24.735 978 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.35 % Allowed : 11.50 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.27), residues: 923 helix: 1.05 (0.25), residues: 401 sheet: -0.44 (0.39), residues: 164 loop : -1.57 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 484 HIS 0.010 0.002 HIS D 207 PHE 0.031 0.003 PHE C 174 TYR 0.016 0.002 TYR D 428 ARG 0.007 0.001 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6803 (mpp) cc_final: 0.5861 (mpp) REVERT: C 306 GLU cc_start: 0.8998 (pt0) cc_final: 0.8679 (tm-30) REVERT: C 449 MET cc_start: 0.8182 (mtp) cc_final: 0.7776 (mmm) REVERT: D 168 MET cc_start: 0.5494 (OUTLIER) cc_final: 0.3004 (mtt) REVERT: D 255 LYS cc_start: 0.5544 (mtmt) cc_final: 0.5133 (mttp) REVERT: D 259 VAL cc_start: 0.8554 (t) cc_final: 0.8265 (m) REVERT: D 484 TRP cc_start: -0.0575 (OUTLIER) cc_final: -0.0857 (m-10) outliers start: 18 outliers final: 11 residues processed: 94 average time/residue: 0.1927 time to fit residues: 25.1771 Evaluate side-chains 85 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 40.0000 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN D 219 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5470 r_free = 0.5470 target = 0.232780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5324 r_free = 0.5324 target = 0.209754 restraints weight = 36470.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.210415 restraints weight = 32860.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5329 r_free = 0.5329 target = 0.211085 restraints weight = 30984.583| |-----------------------------------------------------------------------------| r_work (final): 0.5128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4648 moved from start: 0.7300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 7244 Z= 0.305 Angle : 0.718 6.851 9813 Z= 0.373 Chirality : 0.048 0.295 1116 Planarity : 0.005 0.053 1274 Dihedral : 5.181 27.723 978 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.88 % Allowed : 12.16 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 923 helix: 1.00 (0.25), residues: 405 sheet: -0.45 (0.39), residues: 165 loop : -1.56 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 61 HIS 0.009 0.002 HIS D 207 PHE 0.024 0.002 PHE C 418 TYR 0.020 0.002 TYR C 428 ARG 0.006 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6425 (mpp) cc_final: 0.5449 (mpp) REVERT: C 306 GLU cc_start: 0.8994 (pt0) cc_final: 0.8708 (tm-30) REVERT: C 449 MET cc_start: 0.8122 (mtp) cc_final: 0.7584 (mmm) REVERT: D 168 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.3144 (mtt) REVERT: D 255 LYS cc_start: 0.5902 (mtmt) cc_final: 0.5241 (mttp) REVERT: D 259 VAL cc_start: 0.9006 (t) cc_final: 0.8686 (m) REVERT: D 379 MET cc_start: 0.5652 (ptm) cc_final: 0.5390 (ppp) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.1807 time to fit residues: 24.0405 Evaluate side-chains 88 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 50.0000 chunk 83 optimal weight: 7.9990 chunk 90 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 204 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN D 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.236021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5334 r_free = 0.5334 target = 0.212918 restraints weight = 36403.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.213823 restraints weight = 33068.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.213823 restraints weight = 30702.911| |-----------------------------------------------------------------------------| r_work (final): 0.5091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4508 moved from start: 0.7476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7244 Z= 0.209 Angle : 0.632 6.569 9813 Z= 0.327 Chirality : 0.047 0.313 1116 Planarity : 0.005 0.062 1274 Dihedral : 4.928 26.253 978 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.35 % Allowed : 11.50 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 923 helix: 1.23 (0.26), residues: 410 sheet: -0.31 (0.40), residues: 163 loop : -1.42 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 61 HIS 0.011 0.001 HIS D 115 PHE 0.014 0.002 PHE C 58 TYR 0.014 0.002 TYR D 76 ARG 0.005 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6218 (mpp) cc_final: 0.4255 (mpp) REVERT: C 306 GLU cc_start: 0.8917 (pt0) cc_final: 0.8654 (tm-30) REVERT: C 397 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6754 (mp0) REVERT: C 449 MET cc_start: 0.7996 (mtp) cc_final: 0.7525 (mmm) REVERT: D 123 MET cc_start: 0.1698 (OUTLIER) cc_final: 0.0756 (mmm) REVERT: D 168 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.2794 (mtt) REVERT: D 259 VAL cc_start: 0.8857 (t) cc_final: 0.8545 (m) REVERT: D 261 MET cc_start: 0.3470 (mtp) cc_final: 0.3253 (mtt) REVERT: D 379 MET cc_start: 0.5295 (ptm) cc_final: 0.4990 (ppp) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.1872 time to fit residues: 22.2891 Evaluate side-chains 82 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5461 r_free = 0.5461 target = 0.231637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.208795 restraints weight = 36272.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.209712 restraints weight = 32564.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.5329 r_free = 0.5329 target = 0.210455 restraints weight = 30156.812| |-----------------------------------------------------------------------------| r_work (final): 0.5137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4646 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 7244 Z= 0.262 Angle : 0.678 12.861 9813 Z= 0.346 Chirality : 0.047 0.320 1116 Planarity : 0.005 0.049 1274 Dihedral : 5.082 26.720 978 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.09 % Allowed : 13.46 % Favored : 84.44 % 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: -0.10 (0.28), residues: 923 helix: 1.08 (0.26), residues: 410 sheet: -0.10 (0.41), residues: 162 loop : -1.39 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 61 HIS 0.004 0.001 HIS D 115 PHE 0.023 0.002 PHE D 174 TYR 0.016 0.002 TYR D 76 ARG 0.005 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 PHE cc_start: 0.9031 (m-80) cc_final: 0.8807 (t80) REVERT: C 252 MET cc_start: 0.6398 (mpp) cc_final: 0.4325 (mpp) REVERT: C 397 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6982 (mp0) REVERT: C 449 MET cc_start: 0.8213 (mtp) cc_final: 0.7712 (mmm) REVERT: D 168 MET cc_start: 0.5388 (OUTLIER) cc_final: 0.3023 (mtt) REVERT: D 181 ARG cc_start: -0.5676 (OUTLIER) cc_final: -0.7304 (mmm-85) REVERT: D 259 VAL cc_start: 0.9097 (t) cc_final: 0.8784 (m) REVERT: D 379 MET cc_start: 0.5835 (ptm) cc_final: 0.5236 (ppp) REVERT: D 443 ILE cc_start: 0.8042 (mm) cc_final: 0.7398 (tt) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.2059 time to fit residues: 24.3163 Evaluate side-chains 84 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.222667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.199353 restraints weight = 36911.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5274 r_free = 0.5274 target = 0.200199 restraints weight = 33572.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.5274 r_free = 0.5274 target = 0.200793 restraints weight = 31063.139| |-----------------------------------------------------------------------------| r_work (final): 0.5077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4855 moved from start: 0.9028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 7244 Z= 0.326 Angle : 0.758 7.483 9813 Z= 0.394 Chirality : 0.050 0.421 1116 Planarity : 0.006 0.053 1274 Dihedral : 5.653 27.271 978 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.70 % Allowed : 15.03 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 923 helix: 0.57 (0.25), residues: 410 sheet: -0.27 (0.41), residues: 154 loop : -1.60 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 162 HIS 0.006 0.002 HIS D 219 PHE 0.030 0.003 PHE C 418 TYR 0.019 0.002 TYR C 428 ARG 0.009 0.001 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6433 (mpp) cc_final: 0.4988 (mmm) REVERT: C 449 MET cc_start: 0.8293 (mtp) cc_final: 0.7747 (mmm) REVERT: D 168 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.3098 (mtt) REVERT: D 181 ARG cc_start: -0.4974 (OUTLIER) cc_final: -0.7261 (ttm170) REVERT: D 259 VAL cc_start: 0.9031 (t) cc_final: 0.8733 (m) REVERT: D 261 MET cc_start: 0.3446 (mtt) cc_final: 0.3189 (mtt) REVERT: D 379 MET cc_start: 0.5866 (ptm) cc_final: 0.5407 (ppp) REVERT: D 417 ILE cc_start: 0.2161 (OUTLIER) cc_final: 0.1443 (pt) REVERT: D 443 ILE cc_start: 0.7760 (mm) cc_final: 0.7087 (tt) REVERT: D 469 GLN cc_start: 0.6206 (tp40) cc_final: 0.5936 (pt0) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.1972 time to fit residues: 23.8178 Evaluate side-chains 84 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 0.0270 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 ASN D 219 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5458 r_free = 0.5458 target = 0.228706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.205940 restraints weight = 36562.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.206842 restraints weight = 32582.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.207385 restraints weight = 29856.335| |-----------------------------------------------------------------------------| r_work (final): 0.5131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4651 moved from start: 0.8951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7244 Z= 0.218 Angle : 0.687 8.180 9813 Z= 0.356 Chirality : 0.048 0.397 1116 Planarity : 0.006 0.100 1274 Dihedral : 5.371 31.228 978 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.44 % Allowed : 16.47 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.17 (0.28), residues: 923 helix: 0.98 (0.26), residues: 402 sheet: 0.11 (0.42), residues: 162 loop : -1.48 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 162 HIS 0.006 0.001 HIS D 115 PHE 0.024 0.002 PHE D 215 TYR 0.017 0.002 TYR C 428 ARG 0.004 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6296 (mpp) cc_final: 0.4861 (mpp) REVERT: C 399 LEU cc_start: -0.2530 (OUTLIER) cc_final: -0.2932 (pp) REVERT: C 449 MET cc_start: 0.8009 (mtp) cc_final: 0.7558 (mmm) REVERT: D 115 HIS cc_start: 0.6892 (p-80) cc_final: 0.6405 (p-80) REVERT: D 168 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.2893 (mtt) REVERT: D 181 ARG cc_start: -0.5383 (OUTLIER) cc_final: -0.7373 (ttm170) REVERT: D 379 MET cc_start: 0.5518 (ptm) cc_final: 0.5163 (ppp) REVERT: D 443 ILE cc_start: 0.7769 (mm) cc_final: 0.7160 (tt) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.1853 time to fit residues: 22.7818 Evaluate side-chains 79 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 43 optimal weight: 10.0000 chunk 35 optimal weight: 0.0270 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN C 310 ASN C 421 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.220457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.196235 restraints weight = 37198.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.196981 restraints weight = 33584.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.198009 restraints weight = 31486.931| |-----------------------------------------------------------------------------| r_work (final): 0.5075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4883 moved from start: 0.9778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 7244 Z= 0.326 Angle : 0.789 8.997 9813 Z= 0.407 Chirality : 0.050 0.272 1116 Planarity : 0.006 0.092 1274 Dihedral : 5.823 36.766 978 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.70 % Allowed : 16.73 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.28), residues: 923 helix: 0.59 (0.25), residues: 400 sheet: -0.24 (0.41), residues: 167 loop : -1.62 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 61 HIS 0.007 0.002 HIS D 244 PHE 0.030 0.003 PHE C 418 TYR 0.028 0.003 TYR C 428 ARG 0.009 0.001 ARG C 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6221 (mpp) cc_final: 0.4885 (mmm) REVERT: C 449 MET cc_start: 0.7962 (mtp) cc_final: 0.7506 (mmm) REVERT: D 115 HIS cc_start: 0.6904 (p-80) cc_final: 0.6516 (p-80) REVERT: D 168 MET cc_start: 0.5254 (OUTLIER) cc_final: 0.2835 (mtt) REVERT: D 181 ARG cc_start: -0.4779 (OUTLIER) cc_final: -0.7137 (ttm170) REVERT: D 379 MET cc_start: 0.5787 (ptm) cc_final: 0.5072 (tmm) outliers start: 13 outliers final: 8 residues processed: 80 average time/residue: 0.2153 time to fit residues: 23.4680 Evaluate side-chains 74 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 257 HIS ** 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 = 0.5446 r_free = 0.5446 target = 0.226298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.202029 restraints weight = 36942.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5279 r_free = 0.5279 target = 0.203119 restraints weight = 33801.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.203465 restraints weight = 31028.667| |-----------------------------------------------------------------------------| r_work (final): 0.5124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4749 moved from start: 0.9778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7244 Z= 0.240 Angle : 0.740 9.549 9813 Z= 0.375 Chirality : 0.047 0.169 1116 Planarity : 0.006 0.077 1274 Dihedral : 5.608 41.076 978 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.70 % Allowed : 16.34 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.41 (0.28), residues: 923 helix: 0.85 (0.26), residues: 396 sheet: -0.34 (0.39), residues: 172 loop : -1.49 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 162 HIS 0.007 0.001 HIS D 115 PHE 0.012 0.002 PHE D 174 TYR 0.023 0.002 TYR D 428 ARG 0.004 0.001 ARG D 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2392.18 seconds wall clock time: 44 minutes 49.95 seconds (2689.95 seconds total)