Starting phenix.real_space_refine on Fri Dec 27 23:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izu_61042/12_2024/9izu_61042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izu_61042/12_2024/9izu_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_61042/12_2024/9izu_61042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izu_61042/12_2024/9izu_61042.map" model { file = "/net/cci-nas-00/data/ceres_data/9izu_61042/12_2024/9izu_61042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izu_61042/12_2024/9izu_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.90, per 1000 atoms: 0.69 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: 1.67 Conformation dependent library (CDL) restraints added in 1.1 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: 0.82 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: 1.93 Time building geometry restraints manager: 1.98 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.210 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- 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 : 0.828 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: 0.2741 time to fit residues: 45.5438 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 : 0.804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2115 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 : 0.860 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: -0.1890 (mtt) cc_final: -0.2684 (mtt) REVERT: C 189 LEU cc_start: 0.7110 (mt) cc_final: 0.6871 (mt) REVERT: D 168 MET cc_start: 0.1502 (OUTLIER) cc_final: 0.0539 (mtt) outliers start: 23 outliers final: 9 residues processed: 103 average time/residue: 0.2405 time to fit residues: 32.1206 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 : 0.897 ------------------------------------------------------------------------------- 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 168 MET Chi-restraints excluded: chain D residue 411 TYR 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 46 optimal weight: 5.9990 chunk 26 optimal weight: 0.0020 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 84 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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 256 ASN C 272 GLN C 374 ASN C 421 ASN C 440 ASN C 483 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2247 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7244 Z= 0.251 Angle : 0.655 9.801 9813 Z= 0.335 Chirality : 0.048 0.290 1116 Planarity : 0.005 0.051 1274 Dihedral : 4.552 23.527 978 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.96 % Allowed : 10.33 % 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: 0.03 (0.28), residues: 923 helix: 1.37 (0.25), residues: 417 sheet: -0.32 (0.39), residues: 170 loop : -1.51 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 61 HIS 0.005 0.001 HIS D 219 PHE 0.026 0.002 PHE C 174 TYR 0.011 0.002 TYR C 474 ARG 0.006 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 89 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: -0.1822 (mtt) cc_final: -0.2706 (mtt) REVERT: D 168 MET cc_start: 0.1691 (OUTLIER) cc_final: 0.0338 (mtt) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.2435 time to fit residues: 27.4636 Evaluate side-chains 80 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 83 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 436 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2711 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.144 7244 Z= 0.471 Angle : 0.910 13.933 9813 Z= 0.480 Chirality : 0.054 0.327 1116 Planarity : 0.007 0.062 1274 Dihedral : 5.902 27.915 978 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.14 % Allowed : 10.20 % Favored : 86.67 % 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: -0.91 (0.26), residues: 923 helix: 0.37 (0.24), residues: 399 sheet: -0.61 (0.39), residues: 168 loop : -1.65 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 61 HIS 0.013 0.003 HIS D 207 PHE 0.038 0.004 PHE C 418 TYR 0.017 0.003 TYR D 428 ARG 0.011 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 110 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: -0.1465 (mtt) cc_final: -0.2411 (mtt) REVERT: D 168 MET cc_start: 0.2218 (mmp) cc_final: 0.0717 (mtt) outliers start: 24 outliers final: 13 residues processed: 104 average time/residue: 0.1842 time to fit residues: 26.5657 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 : 0.812 ------------------------------------------------------------------------------- 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 210 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 306 GLU 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 D residue 28 HIS Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 481 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2527 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7244 Z= 0.240 Angle : 0.701 11.711 9813 Z= 0.359 Chirality : 0.048 0.274 1116 Planarity : 0.006 0.086 1274 Dihedral : 5.216 26.124 978 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.61 % Allowed : 12.16 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.27), residues: 923 helix: 0.87 (0.25), residues: 402 sheet: -0.62 (0.40), residues: 155 loop : -1.50 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 61 HIS 0.007 0.002 HIS D 207 PHE 0.023 0.002 PHE D 215 TYR 0.021 0.002 TYR C 428 ARG 0.005 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 99 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: -0.1469 (mtt) cc_final: -0.2500 (mtt) REVERT: D 168 MET cc_start: 0.1587 (OUTLIER) cc_final: 0.0976 (mtt) REVERT: D 193 LEU cc_start: 0.6247 (tp) cc_final: 0.5682 (tp) outliers start: 20 outliers final: 11 residues processed: 92 average time/residue: 0.1841 time to fit residues: 23.3327 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 : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN 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 433 ASP Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 411 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN D 204 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2866 moved from start: 0.9182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 7244 Z= 0.440 Angle : 0.893 8.144 9813 Z= 0.474 Chirality : 0.054 0.323 1116 Planarity : 0.007 0.080 1274 Dihedral : 6.098 27.084 978 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 32.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.18 % Favored : 93.72 % Rotamer: Outliers : 3.01 % Allowed : 13.33 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.26), residues: 923 helix: -0.10 (0.25), residues: 403 sheet: -0.92 (0.39), residues: 150 loop : -1.89 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 61 HIS 0.013 0.003 HIS D 207 PHE 0.044 0.004 PHE C 418 TYR 0.018 0.003 TYR D 428 ARG 0.012 0.001 ARG C 181 *********************** 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 102 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: -0.1182 (mtt) cc_final: -0.2204 (mtt) REVERT: C 294 VAL cc_start: 0.6103 (OUTLIER) cc_final: 0.5834 (t) REVERT: D 168 MET cc_start: 0.2173 (OUTLIER) cc_final: 0.1199 (mtt) REVERT: D 181 ARG cc_start: -0.3436 (OUTLIER) cc_final: -0.6666 (ttm170) REVERT: D 193 LEU cc_start: 0.6762 (tp) cc_final: 0.6408 (tp) outliers start: 23 outliers final: 13 residues processed: 97 average time/residue: 0.2023 time to fit residues: 26.4303 Evaluate side-chains 86 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 466 TYR Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 411 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2560 moved from start: 0.8941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7244 Z= 0.230 Angle : 0.716 8.029 9813 Z= 0.369 Chirality : 0.050 0.389 1116 Planarity : 0.006 0.069 1274 Dihedral : 5.399 26.570 978 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.96 % Allowed : 15.42 % Favored : 82.61 % 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: -0.75 (0.27), residues: 923 helix: 0.48 (0.25), residues: 407 sheet: -0.61 (0.38), residues: 161 loop : -1.54 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 61 HIS 0.006 0.001 HIS D 115 PHE 0.034 0.002 PHE C 174 TYR 0.020 0.002 TYR C 428 ARG 0.005 0.001 ARG D 181 *********************** 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 93 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: -0.1298 (mtt) cc_final: -0.2318 (mtt) REVERT: C 158 MET cc_start: 0.2684 (OUTLIER) cc_final: 0.2407 (ptm) REVERT: D 168 MET cc_start: 0.1685 (OUTLIER) cc_final: 0.0901 (mtt) REVERT: D 181 ARG cc_start: -0.3952 (OUTLIER) cc_final: -0.6896 (ttm170) outliers start: 15 outliers final: 8 residues processed: 89 average time/residue: 0.2144 time to fit residues: 27.3318 Evaluate side-chains 75 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 28 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.0000 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 0.0020 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2610 moved from start: 0.9268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7244 Z= 0.245 Angle : 0.732 8.224 9813 Z= 0.376 Chirality : 0.048 0.314 1116 Planarity : 0.006 0.062 1274 Dihedral : 5.495 35.122 978 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.09 % Allowed : 17.25 % Favored : 80.65 % 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: -0.64 (0.28), residues: 923 helix: 0.54 (0.26), residues: 414 sheet: -0.41 (0.41), residues: 155 loop : -1.53 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 162 HIS 0.006 0.002 HIS D 115 PHE 0.027 0.002 PHE C 174 TYR 0.026 0.002 TYR D 76 ARG 0.005 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 89 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 GLN cc_start: 0.0523 (OUTLIER) cc_final: -0.0864 (pt0) REVERT: C 124 MET cc_start: -0.1452 (mtt) cc_final: -0.2441 (mtt) REVERT: D 135 MET cc_start: 0.5833 (pmm) cc_final: 0.5217 (pmm) REVERT: D 168 MET cc_start: 0.1804 (OUTLIER) cc_final: 0.0825 (mtt) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.1985 time to fit residues: 23.3391 Evaluate side-chains 80 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 28 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0070 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.0370 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN D 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2426 moved from start: 0.9224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 7244 Z= 0.225 Angle : 0.727 9.625 9813 Z= 0.371 Chirality : 0.048 0.232 1116 Planarity : 0.005 0.059 1274 Dihedral : 5.296 34.254 978 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.31 % Allowed : 18.17 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.22 (0.28), residues: 923 helix: 0.86 (0.26), residues: 416 sheet: -0.11 (0.39), residues: 172 loop : -1.40 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 484 HIS 0.008 0.001 HIS D 115 PHE 0.026 0.002 PHE C 174 TYR 0.024 0.002 TYR D 76 ARG 0.003 0.000 ARG C 75 *********************** 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 85 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 GLN cc_start: 0.0236 (OUTLIER) cc_final: -0.1099 (pt0) REVERT: C 124 MET cc_start: -0.1332 (mtt) cc_final: -0.2390 (mtt) REVERT: D 135 MET cc_start: 0.5894 (pmm) cc_final: 0.5387 (pmm) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.2069 time to fit residues: 23.4624 Evaluate side-chains 77 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 98 THR 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 181 ARG Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2930 moved from start: 1.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 7244 Z= 0.467 Angle : 0.940 11.633 9813 Z= 0.491 Chirality : 0.054 0.249 1116 Planarity : 0.007 0.062 1274 Dihedral : 6.367 37.016 978 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 35.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.28 % Favored : 93.61 % Rotamer: Outliers : 1.57 % Allowed : 18.43 % Favored : 80.00 % 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: -1.39 (0.27), residues: 923 helix: -0.29 (0.25), residues: 407 sheet: -0.28 (0.43), residues: 140 loop : -1.82 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP D 61 HIS 0.012 0.003 HIS D 207 PHE 0.029 0.004 PHE C 418 TYR 0.050 0.004 TYR C 428 ARG 0.010 0.002 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 83 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: -0.1345 (mtt) cc_final: -0.2503 (mtt) REVERT: C 128 MET cc_start: 0.1985 (mmt) cc_final: 0.1530 (mmp) REVERT: D 247 ARG cc_start: 0.5086 (OUTLIER) cc_final: 0.3423 (mtt90) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.2111 time to fit residues: 22.9560 Evaluate side-chains 76 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 98 THR 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 181 ARG Chi-restraints excluded: chain D residue 247 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.185059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.158240 restraints weight = 33118.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.159528 restraints weight = 29822.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.160202 restraints weight = 27564.787| |-----------------------------------------------------------------------------| r_work (final): 0.4910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 1.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 7244 Z= 0.343 Angle : 0.832 10.300 9813 Z= 0.429 Chirality : 0.050 0.187 1116 Planarity : 0.006 0.067 1274 Dihedral : 6.206 35.471 978 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.09 % Allowed : 18.17 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.27), residues: 923 helix: -0.17 (0.25), residues: 406 sheet: -0.52 (0.41), residues: 154 loop : -1.68 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 61 HIS 0.008 0.002 HIS D 207 PHE 0.027 0.003 PHE D 164 TYR 0.046 0.003 TYR C 428 ARG 0.009 0.001 ARG C 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1658.71 seconds wall clock time: 31 minutes 49.60 seconds (1909.60 seconds total)